https:/// /w/api.php?action=feedcontributions&feedformat=atom&user=Mkubal 2026-04-30T05:16:37Z User contributions MediaWiki 1.35.6 /w/index.php?title=SeedViewer_Annotation&diff=1585 2006-11-07T20:24:51Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Annotation Page<br /> <br /> Overview<br /> <br /> :This page offers access to the data relating to a feature. By default the Overview version of the page &lt;br&gt;<br /> :is initially displayed providing the feature's function assignment, source organism, the role it performs&lt;br&gt;<br /> :in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one&lt;br&gt;<br /> :or more functional roles, each functional role's name will be displayed and linked to a [[SeedViewer_Functional_Role|SEED Viewer Functional Role page]].<br /> :A part of a feature's function that is not also a functional role is NOT linked. <br /> <br /> :If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box &lt;br&gt;<br /> :at the top of the page on the right. The functional role names and subsystem names are linked to the &lt;br&gt;<br /> :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]].<br /> <br /> :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page&lt;br&gt;<br /> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have&lt;br&gt;<br /> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or &lt;br&gt;<br /> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically&lt;br&gt;<br /> :distant to the subject feature's genome. <br /> :If there are no close genomes only a single line for the subject feature's genome will be present.&lt;br&gt;<br /> :If no data for diverse genomes has been computed a message saying so will be be displayed.&lt;br&gt;<br /> <br /> Sequence Data<br /> <br /> :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the&lt;br&gt;<br /> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. <br /> <br /> Tools<br /> <br /> :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools&lt;br&gt;<br /> :to analyze this feature:&lt;br&gt;<br /> <br /> ::TMpred<br /> ::TMHMM<br /> ::Gram negative PSORT<br /> ::Gram negative SignalP<br /> ::Gram positive PSORT<br /> ::Gram positive SignalP<br /> ::LipoP<br /> ::InterProScan<br /> ::Radar<br /> ::PPSearch<br /> ::Gram negative CELLO<br /> ::Gram positive CELLO<br /> ::ProDom<br /> <br /> Literature<br /> :This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source.</div>

Mkubal /w/index.php?title=SeedViewer_Organism&diff=1584 2006-11-07T20:16:21Z

<p>Mkubal: </p> <hr /> <div>Organism Page in SEED Viewer<br /> <br /> In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu&lt;br&gt;<br /> labeled 'This Organism' with the following 4 display options for this page:&lt;br&gt;<br /> <br /> Overview<br /> :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.&lt;br&gt;<br /> :A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.&lt;br&gt;<br /> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. <br /> :On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem.&lt;br&gt;<br /> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems&lt;br&gt;<br /> :present in this genome by cellular process. <br /> :At every level in the tree the number of protein encoding genes in each category is listed in parentheses.<br /> :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. <br /> <br /> Browse Genome<br /> :This display allows you to walk the chromosome of the selected genome.&lt;br&gt;<br /> :If the genome is not completely assembled, the first contig will be selected.<br /> :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.&lt;br&gt;<br /> :The &lt; and &gt; buttons will move the window down or up the chromosome half the window size.&lt;br&gt;<br /> :The &lt;&lt; and &gt;&gt; buttons will move the window down or up the chromosome a full window size.&lt;br&gt;<br /> :Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism.&lt;br&gt;<br /> :After selecting your options, click the 'Refresh' button to update the page.<br /> :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.&lt;br&gt;<br /> :Hover over a feature in the chromosome display for a detailed description. <br /> :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.<br /> <br /> View Features<br /> :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative&lt;br&gt;<br /> :to the beginning of the contig, feature type and a list of aliases.&lt;br&gt;<br /> :The total number of features for this genome is displayed above the table.&lt;br&gt;<br /> :Use the 'next&gt;&gt;' and 'last&gt;&gt;' links to quickly scroll through sets of 10 features.&lt;br&gt;<br /> :Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter.<br /> :Sort or reverse sort the tables using the triangle in the columns headers.<br /> :Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button.<br /> <br /> View Reactions</div>

Mkubal /w/index.php?title=SeedViewer_Home&diff=1583 2006-11-07T20:09:34Z

<p>Mkubal: </p> <hr /> <div>===Counts of Genomes in the SEED===<br /> <br /> The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.&lt;br&gt;<br /> A box on the top right of the home page provides a current total and complete count of each type.&lt;br&gt;<br /> Click on archael, bacterial, eukaryal, or viral to display a table listing the genomes in this set.&lt;br&gt;<br /> <br /> <br /> ===Searching===<br /> <br /> The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.&lt;br&gt;<br /> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.&lt;br&gt;<br /> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives.<br /> <br /> Text Search&lt;br&gt;<br /> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.&lt;br&gt;<br /> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features.<br /> :The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.&lt;br&gt;<br /> :If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables&lt;br&gt;<br /> :mentioned above will not be displayed.<br /> :The number of hits associated with a functional role will appear above the Functional Role table. &lt;br&gt;<br /> :The number of features returned is limited to 100. &lt;br&gt;<br /> :To browse the results quickly use the next &gt;&gt; and last &gt;&gt; links. <br /> :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.&lt;br&gt;<br /> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem.<br /> :In any of the results tables,<br /> :clicking on a functional role will take you to a Functional Role page in the SEED Viewer,<br /> :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and<br /> :clicking on a feature ID will take you an Annotation page in the SEED Viewer.<br /> <br /> Blast Search&lt;br&gt;<br /> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.&lt;br&gt;<br /> : Then click the 'Blast Search' button to the right of the genome pulldown menu. <br /> : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer.<br /> <br /> Subsystems Search&lt;br&gt;<br /> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the subsystem name.<br /> :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer.<br /> <br /> Organism Search&lt;br&gt;<br /> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the genome.<br /> :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer.</div>

Mkubal /w/index.php?title=SeedViewer_Home&diff=1582 2006-11-07T20:08:31Z

<p>Mkubal: </p> <hr /> <div>===Counts of Genomes in the SEED===<br /> <br /> The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.&lt;br&gt;<br /> A box on the top right of the home page provides a current total and complete count of each type.&lt;br&gt;<br /> Click on archael, bacterial. eukaryal, or viral to display a table listing the genomes in this set.&lt;br&gt;<br /> <br /> <br /> ===Searching===<br /> <br /> The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.&lt;br&gt;<br /> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.&lt;br&gt;<br /> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives.<br /> <br /> Text Search&lt;br&gt;<br /> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.&lt;br&gt;<br /> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features.<br /> :The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.&lt;br&gt;<br /> :If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables&lt;br&gt;<br /> :mentioned above will not be displayed.<br /> :The number of hits associated with a functional role will appear above the Functional Role table. &lt;br&gt;<br /> :The number of features returned is limited to 100. &lt;br&gt;<br /> :To browse the results quickly use the next &gt;&gt; and last &gt;&gt; links. <br /> :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.&lt;br&gt;<br /> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem.<br /> :In any of the results tables,<br /> :clicking on a functional role will take you to a Functional Role page in the SEED Viewer,<br /> :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and<br /> :clicking on a feature ID will take you an Annotation page in the SEED Viewer.<br /> <br /> Blast Search&lt;br&gt;<br /> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.&lt;br&gt;<br /> : Then click the 'Blast Search' button to the right of the genome pulldown menu. <br /> : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer.<br /> <br /> Subsystems Search&lt;br&gt;<br /> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the subsystem name.<br /> :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer.<br /> <br /> Organism Search&lt;br&gt;<br /> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the genome.<br /> :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer.</div>

Mkubal /w/index.php?title=SeedViewer_Home&diff=1581 2006-11-07T20:08:11Z

<p>Mkubal: </p> <hr /> <div>===Counts of Genomes in the SEED===<br /> <br /> The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.&lt;br&gt;<br /> A box on the top right of the home page provides a current total and complete count of each type. &lt;&gt;br&gt;<br /> Click on archael, bacterial. eukaryal, or viral to display a table listing the genomes in this set.&lt;br&gt;<br /> <br /> <br /> ===Searching===<br /> <br /> The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.&lt;br&gt;<br /> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.&lt;br&gt;<br /> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives.<br /> <br /> Text Search&lt;br&gt;<br /> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.&lt;br&gt;<br /> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features.<br /> :The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.&lt;br&gt;<br /> :If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables&lt;br&gt;<br /> :mentioned above will not be displayed.<br /> :The number of hits associated with a functional role will appear above the Functional Role table. &lt;br&gt;<br /> :The number of features returned is limited to 100. &lt;br&gt;<br /> :To browse the results quickly use the next &gt;&gt; and last &gt;&gt; links. <br /> :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.&lt;br&gt;<br /> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem.<br /> :In any of the results tables,<br /> :clicking on a functional role will take you to a Functional Role page in the SEED Viewer,<br /> :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and<br /> :clicking on a feature ID will take you an Annotation page in the SEED Viewer.<br /> <br /> Blast Search&lt;br&gt;<br /> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.&lt;br&gt;<br /> : Then click the 'Blast Search' button to the right of the genome pulldown menu. <br /> : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer.<br /> <br /> Subsystems Search&lt;br&gt;<br /> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the subsystem name.<br /> :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer.<br /> <br /> Organism Search&lt;br&gt;<br /> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the genome.<br /> :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer.</div>

Mkubal /w/index.php?title=SeedViewer_Annotation&diff=1580 2006-11-07T20:03:35Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Annotation Page<br /> <br /> Overview<br /> <br /> :This page offers access to the data relating to a feature. By default the Overview version of the page &lt;br&gt;<br /> :is initially displayed providing the feature's function assignment, source organism, the role it performs&lt;br&gt;<br /> :in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one&lt;br&gt;<br /> :or more functional roles, each functional role's name will be displayed and linked to a [[SeedViewer_Functional_Role|SEED Viewer Functional Role page]].<br /> :A part of a feature's function that is not also a functional role is NOT linked. <br /> <br /> :If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box &lt;br&gt;<br /> :at the top of the page on the right. The functional role names and subsystem names are linked to the &lt;br&gt;<br /> :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]].<br /> <br /> :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page&lt;br&gt;<br /> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have&lt;br&gt;<br /> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or &lt;br&gt;<br /> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically&lt;br&gt;<br /> :distant to the subject feature's genome.<br /> <br /> Sequence Data<br /> <br /> :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the&lt;br&gt;<br /> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. <br /> <br /> Tools<br /> <br /> :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools&lt;br&gt;<br /> :to analyze this feature:&lt;br&gt;<br /> <br /> ::TMpred<br /> ::TMHMM<br /> ::Gram negative PSORT<br /> ::Gram negative SignalP<br /> ::Gram positive PSORT<br /> ::Gram positive SignalP<br /> ::LipoP<br /> ::InterProScan<br /> ::Radar<br /> ::PPSearch<br /> ::Gram negative CELLO<br /> ::Gram positive CELLO<br /> ::ProDom<br /> <br /> Literature<br /> :This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source.</div>

Mkubal /w/index.php?title=SeedViewer_Annotation&diff=1579 2006-11-07T20:00:46Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Annotation Page<br /> <br /> Overview<br /> <br /> :This page offers access to the data relating to a feature. By default the Overview version of the page &lt;br&gt;<br /> :is initially displayed providing the feature's function assignment, source organism, the role it performs&lt;br&gt;<br /> :in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one&lt;br&gt;<br /> :or more functional roles, each functional role's name will be displayed and linked to a [[SeedViewer_Functional_Role|SEED Viewer Functional Role page]].<br /> :A part of a feature's function that is not also a functional role is NOT linked. <br /> <br /> :If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box &lt;br&gt;<br /> :at the top of the page on the right. The functional role names and subsystem names are linked to the &lt;br&gt;<br /> :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]].<br /> <br /> :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page&lt;br&gt;<br /> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have&lt;br&gt;<br /> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or &lt;br&gt;<br /> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically&lt;br&gt;<br /> :distant to the subject feature's genome.<br /> <br /> Sequence Data<br /> <br /> :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the&lt;br&gt;<br /> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. <br /> <br /> Tools<br /> <br /> :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools&lt;br&gt;<br /> :to analyze this feature:&lt;br&gt;<br /> <br /> ::TMpred<br /> ::TMHMM<br /> ::Gram negative PSORT<br /> ::Gram negative SignalP<br /> ::Gram positive PSORT<br /> ::Gram positive SignalP<br /> ::LipoP<br /> ::InterProScan<br /> ::Radar<br /> ::PPSearch<br /> ::Gram negative CELLO<br /> ::Gram positive CELLO<br /> ::ProDom<br /> <br /> Literature</div>

Mkubal /w/index.php?title=SeedViewer_Annotation&diff=1578 2006-11-07T19:54:13Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Annotation Page<br /> <br /> Overview<br /> <br /> :This page offers access to the data relating to a feature. By default the Overview version of the page &lt;br&gt;<br /> :is initially displayed providing the feature's function assignment, source organism, the role it performs&lt;br&gt;<br /> :in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one&lt;br&gt;<br /> :or more functional roles, each functional role's name will be displayed and linked to a [[SeedViewer_Functional_Role|SEED Viewer Functional Role page]].<br /> <br /> :If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box &lt;br&gt;<br /> :at the top of the page on the right. The functional role names and subsystem names are linked to the &lt;br&gt;<br /> :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]].<br /> <br /> :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page&lt;br&gt;<br /> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have&lt;br&gt;<br /> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or &lt;br&gt;<br /> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically&lt;br&gt;<br /> :distant to the subject feature's genome.<br /> <br /> Sequence Data<br /> <br /> :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the&lt;br&gt;<br /> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. <br /> <br /> Tools<br /> <br /> :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools&lt;br&gt;<br /> :to analyze this feature:&lt;br&gt;<br /> <br /> ::TMpred<br /> ::TMHMM<br /> ::Gram negative PSORT<br /> ::Gram negative SignalP<br /> ::Gram positive PSORT<br /> ::Gram positive SignalP<br /> ::LipoP<br /> ::InterProScan<br /> ::Radar<br /> ::PPSearch<br /> ::Gram negative CELLO<br /> ::Gram positive CELLO<br /> ::ProDom<br /> <br /> Literature</div>

Mkubal /w/index.php?title=SeedViewer_Annotation&diff=1577 2006-11-07T19:45:39Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Annotation Page<br /> <br /> Overview<br /> <br /> :This page offers access to the data relating to a feature. By default the Overview version of the page &lt;br&gt;<br /> :is initially displayed providing the feature's function assignment, source organism, the role it performs&lt;br&gt;<br /> :in a subsystem, and a graphic displaying it's genomic context.<br /> <br /> :Detailed information about this feature's role or roles in one or more subsystems is provided in a shaded&lt;br&gt;<br /> :at the top of the page on the right. The functional role names and subsystem names are linked to the &lt;br&gt;<br /> :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]].<br /> <br /> :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page&lt;br&gt;<br /> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have&lt;br&gt;<br /> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or &lt;br&gt;<br /> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically&lt;br&gt;<br /> :distant to the subject feature's genome.<br /> <br /> Sequence Data<br /> <br /> :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the&lt;br&gt;<br /> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. <br /> <br /> Tools<br /> <br /> :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools&lt;br&gt;<br /> :to analyze this feature:&lt;br&gt;<br /> <br /> ::TMpred<br /> ::TMHMM<br /> ::Gram negative PSORT<br /> ::Gram negative SignalP<br /> ::Gram positive PSORT<br /> ::Gram positive SignalP<br /> ::LipoP<br /> ::InterProScan<br /> ::Radar<br /> ::PPSearch<br /> ::Gram negative CELLO<br /> ::Gram positive CELLO<br /> ::ProDom<br /> <br /> Literature</div>

Mkubal /w/index.php?title=SeedViewer_Home&diff=1576 2006-11-07T19:37:16Z

<p>Mkubal: </p> <hr /> <div>===Counts of Genomes in the SEED===<br /> <br /> The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.&lt;br&gt;<br /> A box on the top right of the home page provides a current total and complete count of each type.<br /> <br /> ===Searching===<br /> <br /> The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.&lt;br&gt;<br /> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.&lt;br&gt;<br /> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives.<br /> <br /> Text Search&lt;br&gt;<br /> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.&lt;br&gt;<br /> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features.<br /> :The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.&lt;br&gt;<br /> :If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables&lt;br&gt;<br /> :mentioned above will not be displayed.<br /> :The number of hits associated with a functional role will appear above the Functional Role table. &lt;br&gt;<br /> :The number of features returned is limited to 100. &lt;br&gt;<br /> :To browse the results quickly use the next &gt;&gt; and last &gt;&gt; links. <br /> :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.&lt;br&gt;<br /> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem.<br /> :In any of the results tables,<br /> :clicking on a functional role will take you to a Functional Role page in the SEED Viewer,<br /> :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and<br /> :clicking on a feature ID will take you an Annotation page in the SEED Viewer.<br /> <br /> Blast Search&lt;br&gt;<br /> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.&lt;br&gt;<br /> : Then click the 'Blast Search' button to the right of the genome pulldown menu. <br /> : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer.<br /> <br /> Subsystems Search&lt;br&gt;<br /> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the subsystem name.<br /> :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer.<br /> <br /> Organism Search&lt;br&gt;<br /> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the genome.<br /> :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer.</div>

Mkubal /w/index.php?title=SeedViewer_Home&diff=1575 2006-11-07T19:35:18Z

<p>Mkubal: </p> <hr /> <div>===Counts of Genomes in the SEED===<br /> <br /> The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.&lt;br&gt;<br /> A box on the top right of the home page provides a current total and complete count of each type.<br /> <br /> ===Searching===<br /> <br /> The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.&lt;br&gt;<br /> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.&lt;br&gt;<br /> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives.<br /> <br /> Text Search&lt;br&gt;<br /> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.&lt;br&gt;<br /> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features.<br /> :The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.&lt;br&gt;<br /> :If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables&lt;br&gt;<br /> :mentioned above will not be displayed.<br /> :The number of hits associated with a functional role will appear above the Functional Role table. &lt;br&gt;<br /> :The number of features returned is limited to 100. &lt;br&gt;<br /> :To browse the results quickly use the next &gt;&gt; and last &gt;&gt; links. <br /> :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.&lt;br&gt;<br /> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem.<br /> :In any of the results tables,<br /> :clicking on a functional role will take you to a Functional Role page in the SEED Viewer,<br /> :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and<br /> :clicking on a PEG ID will take you an Annotation page in the SEED Viewer.<br /> <br /> Blast Search&lt;br&gt;<br /> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.&lt;br&gt;<br /> : Then click the 'Blast Search' button to the right of the genome pulldown menu. <br /> : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer.<br /> <br /> Subsystems Search&lt;br&gt;<br /> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the subsystem name.<br /> :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer.<br /> <br /> Organism Search&lt;br&gt;<br /> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the genome.<br /> :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer.</div>

Mkubal /w/index.php?title=SeedViewer_Functional_Role&diff=1574 2006-11-07T19:23:56Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Functional Role Page<br /> <br /> <br /> In the top right corner of this page are statistics on the number of protein encoding genes within the SEED database that currently are&lt;br&gt;<br /> associated with this functional role and within how many different organisms these genes are present.<br /> <br /> <br /> This page list the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction.<br /> <br /> <br /> A table list all occurences of the functional role in the SEED database. Click [[SeedViewer_HowTo|here ]] for table manipulation tips.</div>

Mkubal /w/index.php?title=SeedViewer_Functional_Role&diff=1573 2006-11-07T19:22:09Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Functional Role Page<br /> <br /> In the top right corner of this page are statistics on the number of protein encoding genes within the SEED database that currently are&lt;br&gt;<br /> associated with this functional role and within how many different organisms these genes are present.<br /> <br /> This page list the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction.<br /> <br /> A table list all occurences of the functional role in the SEED database. Refer to [[]SeedViewer_HowTo]] for table manipulation.</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1572 2006-11-07T19:09:39Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.&lt;br&gt;<br /> or to return to the 'Overview'.<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :The taxonomy ID in the organism column is linked to an Organism page in the SEED Viewer.&lt;br&gt; <br /> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. <br /> :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress' and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.&lt;br&gt;<br /> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented)&lt;br&gt;<br /> <br /> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.&lt;br&gt;<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.&lt;br&gt;<br /> <br /> Notes<br /> :The notes page contains explanations of the variant codes, references and additional information about this subsystem.</div>

Mkubal /w/index.php?title=SeedViewer_Functional_Role&diff=1571 2006-11-07T19:07:08Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Functional Role Page<br /> <br /> In the top right corner of this page are statistics on the number of protein encoding genes within the SEED database that currently are&lt;br&gt;<br /> associated with this functional role and within how many different organisms these genes are present.</div>

Mkubal /w/index.php?title=SeedViewer_HowTo&diff=1570 2006-11-07T19:05:30Z

<p>Mkubal: </p> <hr /> <div>===General Features and Conventions of SeedViewer===<br /> :Menus in the green bar at the top of every SEED Viewer page list options for interacting with the page.<br /> :Tool tips - [?] indicates a tool tip will appear when hovered above with the mouse. Underlined [?] indicates a clickable tool tip &lt;br&gt;<br /> :that also links into a wiki page for a more detailed explanation<br /> <br /> :Text Entry Boxes - if the text box has a pulldown menu beneath it, as text is entered in the box the menu will be updated with only items&lt;br&gt;<br /> :that match or contain the entered text.<br /> <br /> :Filtering Table Entries - filter the table by typing in text entry boxes in the column headers and hitting enter. Table entries that contain the typed text&lt;br&gt;<br /> :will remain. <br /> <br /> :Sorting Table Entries - alpahnumerically sort or reverse sort with the respective triangle in a column header<br /> <br /> :Browsing Table Entries - use the next&gt;&gt; and last&gt;&gt; links to quickly browse tables with more than 10 rows <br /> <br /> ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:===<br /> <br /> :[[SeedViewer_Home| Home page]]<br /> <br /> :[[SeedViewer_Organism| Organism page]]<br /> <br /> :[[SeedViewer_Annotation| Annotation page]]<br /> <br /> :[[SeedViewer_Functional_Role| Functional Role page]]<br /> <br /> :[[SeedViewer_Subsystem| Subsystem page]]<br /> <br /> ===For tutorials on accomplishing specific tasks, please follow the link below:===<br /> <br /> :[[SeedViewer_Tutorial| Tutorials]]</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1569 2006-11-07T18:56:47Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.&lt;br&gt;<br /> or to return to the 'Overview'.<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. <br /> :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress' and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.&lt;br&gt;<br /> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented)&lt;br&gt;<br /> <br /> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.&lt;br&gt;<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.&lt;br&gt;<br /> <br /> Notes<br /> :The notes page contains explanations of the variant codes, references and additional information about this subsystem.</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1568 2006-11-07T18:54:42Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.&lt;br&gt;<br /> or to return to the 'Overview'.<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. <br /> :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress' and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.&lt;br&gt;<br /> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented.Br&gt;<br /> <br /> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.&lt;br&gt;<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.&lt;br&gt;<br /> <br /> Notes<br /> :The notes page contains explanations of the variant codes, references and additional information about this subsystem.</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1567 2006-11-07T18:52:18Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.&lt;br&gt;<br /> or to return to the 'Overview'.<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. <br /> :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'&lt;br&gt;<br /> :and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.&lt;br&gt;<br /> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented.Br&gt;<br /> <br /> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.&lt;br&gt;<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.&lt;br&gt;<br /> <br /> Notes<br /> :The notes page contains explanations of the variant codes, references and additional information about this subsystem.</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1566 2006-11-07T18:51:21Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Use the 'This Subsystem' menu in the green bar at the top of the page to view the 'Populated Subsystem' spreadsheet or to 'View Notes' for this susbystem.&lt;br&gt;<br /> or to return to the 'Overview'.<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. <br /> :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'&lt;br&gt;<br /> :and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.&lt;br&gt;<br /> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented.Br&gt;<br /> <br /> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.&lt;br&gt;<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.&lt;br&gt;<br /> <br /> Notes<br /> :The notes page contains explanations of the variant codes, references and additional information about this subsystem.</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1565 2006-11-07T18:50:50Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Use the 'This Subsystem' menu in the green bar at the top of the page to view the Populated Subsystem spreadsheet or to 'View Notes' for this susbystem.&lt;br&gt;<br /> or return to the 'Overview'.<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. <br /> :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'&lt;br&gt;<br /> :and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.&lt;br&gt;<br /> :Use the 'Collapse/Expand Group Aliases' button to combine or separate columns that are in the same group.(not yet implemented.Br&gt;<br /> <br /> :Hovering over any element in a cell will display the SEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.&lt;br&gt;<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.&lt;br&gt;<br /> <br /> Notes<br /> :The notes page contains explanations of the variant codes, references and additional information about this subsystem.</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1564 2006-11-07T18:40:31Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :An explanation of number in the Variant column is found by selecting 'View Notes' under the 'This Subsystem' menu in the green bar at the top of the page. <br /> :At the bottom of the page, checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'&lt;br&gt;<br /> :and clicking the 'Refresh populated subsystem' button, will update the spreadsheet with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.&lt;br&gt;<br /> <br /> :Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.&lt;br&gt;<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.&lt;br&gt;<br /> <br /> Notes</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1563 2006-11-07T17:51:46Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :By checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'&lt;br&gt;<br /> :and clicking the 'Refresh populated subsystem' button, the spreadsheet will be updated with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.&lt;br&gt;<br /> <br /> :Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.&lt;br&gt;<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.&lt;br&gt;<br /> <br /> Notes</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1562 2006-11-07T17:51:23Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :By checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'&lt;br&gt;<br /> :and clicking the 'Refresh populated subsystem' button, the spreadsheet will be updated with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.&lt;br&gt;<br /> <br /> :Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes.&lt;br&gt;<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem&lt;br&gt;.<br /> <br /> Notes</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1561 2006-11-07T17:50:46Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :By checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'&lt;br&gt;<br /> :and clicking the 'Refresh populated subsystem' button, the spreadsheet will be updated with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms.&lt;br&gt;<br /> <br /> :Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes&lt;br&gt;.<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br /> <br /> Notes</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1560 2006-11-07T17:50:19Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :By checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'&lt;br&gt;<br /> :and clicking the 'Refresh populated subsystem' button, the spreadsheet will be updated with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms&lt;br&gt;.<br /> <br /> :Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes&lt;br&gt;.<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br /> <br /> Notes</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1559 2006-11-07T17:49:56Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight the roles in the table that define internal pathways of the subsystem.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :By default this spreadsheet shows only genomes that possess a functional variant of this subsystem.&lt;br&gt;<br /> :By checking the box 'Show organisms classified as not present in this subsystem' or 'Show organisms classified as work in progress'&lt;br&gt;<br /> :and clicking the 'Refresh populated subsystem' button, the spreadsheet will be updated with these genomes.&lt;br&gt;<br /> :Use the 'Limit genomes by taxonomy' menu, followed by the refresh button to limit the table to a specific group of organisms&lt;br&gt;.<br /> <br /> ::Hovering over any element in a cell will display the SEEED ID(s) of the gene(s) it contains .&lt;br&gt;<br /> :Spreadsheet cells in the same row that contain rectangles of the same color represent genes that are clustered.&lt;br&gt;<br /> :A colored rectangle with an adjacent triangle indicate multiple genes are associated with this role.&lt;br&gt;<br /> :A white rectangle with a number indicates an unclustered gene(s) is associated with this role. The number indicates the number of genes&lt;br&gt;.<br /> :A black triangle indicates that there are more than five clusters of genes present in this genome for this subsystem.<br /> <br /> Notes</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1558 2006-11-07T17:15:41Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> :they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.&lt;br&gt;<br /> :If the annotator of the subsytem has defined subsets of functional roles, the 'Highlight subsets' menu will be present above the table. Use this menu&lt;br&gt;<br /> :to highlight defined internal pathways of the subsystem in within the table.&lt;br&gt; <br /> <br /> Populated Subsystem<br /> :<br /> <br /> <br /> Notes</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1557 2006-11-07T17:03:36Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Overview<br /> :On the top, right of the page a box contains the statistics for this subsystem including the&lt;br&gt;<br /> :number of functional roles, total number of genomes, and the number of genomes where this subsystem&lt;br&gt;<br /> :is present,not present or is still a work in progress.<br /> <br /> :The username of annotator who is responsible for the subsystem is listed.<br /> <br /> Diagram<br /> :The noninteractive diagram illustrates the connectivity of the roles, alternate pathways, intermediate compounds and cofactors.<br /> :The functional role abbreviations in the boxes reference the roles in the table below. Currently diagrams are not present for every subsystem. <br /> <br /> Functional Roles Table<br /> :This list all the functional roles that define the subsystem. Each functional role is linked to a Functional Role page in the SEED Viewer.&lt;br&gt;<br /> :When present the entry in the EC column links to KEGG. <br /> :In the Ontologies column, the buttons 'Rc' and 'GO' are shaded green if a KEGG reaction&lt;br&gt;<br /> :or GO ontology term respectively is associated with this functional role. The 'Rc' button is linked to back to the Functional Role page&lt;br&gt;<br /> :which displays the KEGG reaction id. The 'GO' button is linked to an entry in AmiGO. <br /> :Functional roles that share the same abbreviation in the Group Alias column have been grouped together by the annotator, usually because&lt;br&gt;<br /> they share a similar function but are found in different organisms. These groupings can be utilized in visualizing the Populated Subsystem table.<br /> <br /> Populated Subsystem<br /> :<br /> <br /> <br /> Notes</div>

Mkubal /w/index.php?title=SeedViewer_Subsystem&diff=1556 2006-11-03T21:08:00Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Subsystem Page<br /> <br /> Overview<br /> :Statistics<br /> :Functional Roles Table<br /> <br /> Populated Subsystem<br /> <br /> Notes</div>

Mkubal /w/index.php?title=SeedViewer_Functional_Role&diff=1555 2006-11-03T21:03:41Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Functional Role Page<br /> <br /> In the top right corner of this page are statistics on the number of PEGs within the SEED database that currently are&lt;br&gt;<br /> associated with this functional role and within how many different organisms these PEGs are present.</div>

Mkubal /w/index.php?title=SeedViewer_Annotation&diff=1554 2006-11-03T20:51:06Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Annotation Page<br /> <br /> Overview<br /> <br /> :This page offers access to the data relating to a feature. By default the Overview version of the page &lt;br&gt;<br /> :is initially displayed providing the feature's function assignment, source organism, the role it performs&lt;br&gt;<br /> :in a subsystem, and a graphic displaying it's genomic context.<br /> <br /> :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page&lt;br&gt;<br /> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have&lt;br&gt;<br /> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or &lt;br&gt;<br /> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically&lt;br&gt;<br /> :distant to the subject feature's genome.<br /> <br /> Sequence Data<br /> <br /> :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the&lt;br&gt;<br /> :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. <br /> <br /> Tools<br /> <br /> :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools&lt;br&gt;<br /> :to analyze this feature:&lt;br&gt;<br /> <br /> ::TMpred<br /> ::TMHMM<br /> ::Gram negative PSORT<br /> ::Gram negative SignalP<br /> ::Gram positive PSORT<br /> ::Gram positive SignalP<br /> ::LipoP<br /> ::InterProScan<br /> ::Radar<br /> ::PPSearch<br /> ::Gram negative CELLO<br /> ::Gram positive CELLO<br /> ::ProDom<br /> <br /> Literature</div>

Mkubal /w/index.php?title=SeedViewer_Annotation&diff=1553 2006-11-03T20:48:40Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Annotation Page<br /> <br /> Overview<br /> <br /> :This page offers access to the data relating to a feature. By default the Overview version of the page &lt;br&gt;<br /> :is initially displayed providing the feature's function assignment, source organism, the role it performs&lt;br&gt;<br /> :in a subsystem, and a graphic displaying it's genomic context.<br /> <br /> :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page&lt;br&gt;<br /> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have&lt;br&gt;<br /> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or &lt;br&gt;<br /> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically&lt;br&gt;<br /> :distant to the subject feature's genome.<br /> <br /> Sequence Data<br /> <br /> :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the&lt;br&gt;<br /> this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. <br /> <br /> Tools<br /> <br /> :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools&lt;br&gt;<br /> :to analyze this feature:&lt;br&gt;<br /> <br /> ::TMpred<br /> ::TMHMM<br /> ::Gram negative PSORT<br /> ::Gram negative SignalP<br /> ::Gram positive PSORT<br /> ::Gram positive SignalP<br /> ::LipoP<br /> ::InterProScan<br /> ::Radar<br /> ::PPSearch<br /> ::Gram negative CELLO<br /> ::Gram positive CELLO<br /> ::ProDom<br /> <br /> Literature</div>

Mkubal /w/index.php?title=SeedViewer_Annotation&diff=1552 2006-11-03T20:46:58Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Annotation Page<br /> <br /> Overview<br /> <br /> :This page offers access to the data relating to a feature. By default the Overview version of the page &lt;br&gt;<br /> :is initially displayed providing the feature's function assignment, source organism, the role it performs&lt;br&gt;<br /> :in a subsystem, and a graphic displaying it's genomic context.<br /> <br /> :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page&lt;br&gt;<br /> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have&lt;br&gt;<br /> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or &lt;br&gt;<br /> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically&lt;br&gt;<br /> :distant to the subject feature's genome.<br /> <br /> Sequence Data<br /> <br /> :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the&lt;br&gt;<br /> this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. <br /> <br /> Tools<br /> <br /> :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools&lt;br&gt;<br /> :to analyze this feature:&lt;br&gt;<br /> <br /> ::TMpred<br /> :TMHMM<br /> :Gram negative PSORT<br /> :Gram negative SignalP<br /> :Gram positive PSORT<br /> :Gram positive SignalP<br /> :LipoP<br /> :InterProScan<br /> :Radar<br /> :PPSearch<br /> :Gram negative CELLO<br /> :Gram positive CELLO<br /> :ProDom<br /> <br /> Literature</div>

Mkubal /w/index.php?title=SeedViewer_HowTo&diff=1551 2006-11-03T20:46:03Z

<p>Mkubal: </p> <hr /> <div>===General Features and Conventions of SeedViewer===<br /> :Tool tips - [?] indicates a tool tip will appear when hovered above with the mouse. Underlined [?] indicates a clickable tool tip &lt;br&gt;<br /> :that also links into a wiki page for a more detailed explanation<br /> <br /> :Text Entry Boxes - if the text box has a pulldown menu beneath it, as text is entered in the box the menu will be updated with only items&lt;br&gt;<br /> :that match or contain the entered text.<br /> <br /> :Sorting Table Entries - alpahnumerically sort or reverse sort with the respective triangle in a column header<br /> <br /> :Browsing Table Entries - use the next&gt;&gt; and last&gt;&gt; links to quickly browse tables with more than 10 rows <br /> <br /> ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:===<br /> <br /> :[[SeedViewer_Home| Home page]]<br /> <br /> :[[SeedViewer_Organism| Organism page]]<br /> <br /> :[[SeedViewer_Annotation| Annotation page]]<br /> <br /> :[[SeedViewer_Functional_Role| Functional Role page]]<br /> <br /> :[[SeedViewer_Subsystem| Subsystem page]]<br /> <br /> ===For tutorials on accomplishing specific tasks, please follow the link below:===<br /> <br /> :[[SeedViewer_Tutorial| Tutorials]]</div>

Mkubal /w/index.php?title=SeedViewer_Search&diff=1550 2006-11-03T20:44:31Z

<p>Mkubal: </p> <hr /> <div>SEED Viewer Annotation Page<br /> <br /> Overview<br /> <br /> :This page offers access to the data relating to a feature. By default the Overview version of the page &lt;br&gt;<br /> :is initially displayed providing the feature's function assignment, source organism, the role it performs&lt;br&gt;<br /> :in a subsystem, and a graphic displaying it's genomic context.<br /> <br /> :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page&lt;br&gt;<br /> :is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have&lt;br&gt;<br /> :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or &lt;br&gt;<br /> :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically&lt;br&gt;<br /> :distant to the subject feature's genome.<br /> <br /> Sequence Data<br /> <br /> :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the&lt;br&gt;<br /> this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. <br /> <br /> Tools<br /> <br /> :From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools&lt;br&gt;<br /> :to analyze this feature:&lt;br&gt;<br /> <br /> ::TMpred<br /> :TMHMM<br /> :Gram negative PSORT<br /> :Gram negative SignalP<br /> :Gram positive PSORT<br /> :Gram positive SignalP<br /> :LipoP<br /> :InterProScan<br /> :Radar<br /> :PPSearch<br /> :Gram negative CELLO<br /> :Gram positive CELLO<br /> :ProDom<br /> <br /> Literature</div>

Mkubal /w/index.php?title=SeedViewer_Organism&diff=1549 2006-11-03T19:48:46Z

<p>Mkubal: </p> <hr /> <div>Organism Page in SEED Viewer<br /> <br /> In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu&lt;br&gt;<br /> labeled 'This Organism' with the following 4 display options for this page:&lt;br&gt;<br /> <br /> Overview<br /> :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.&lt;br&gt;<br /> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.&lt;br&gt;<br /> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. <br /> :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.&lt;br&gt;<br /> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems&lt;br&gt;<br /> :present in this genome by cellular process. <br /> :At every level in the tree the number of PEGs in each category is listed in parentheses.<br /> :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. <br /> <br /> Browse Genome<br /> :This display allows you to walk the chromosome of the selected genome.&lt;br&gt;<br /> :If the genome is not completely assembled, the first contig will be selected.<br /> :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.&lt;br&gt;<br /> :The &lt; and &gt; buttons will move the window down or up the chromosome half the window size.&lt;br&gt;<br /> :The &lt;&lt; and &gt;&gt; buttons will move the window down or up the chromosome a full window size.&lt;br&gt;<br /> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.&lt;br&gt;<br /> :After selecting your options, click the 'Refresh' button to update the page.<br /> :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.&lt;br&gt;<br /> :Hover over a feature in the chromosome display for a detailed description. <br /> :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.<br /> <br /> View Features<br /> :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative&lt;br&gt;<br /> :to the beginning of the contig, feature type and a list of aliases.&lt;br&gt;<br /> :The total number of features for this genome is displayed above the table.&lt;br&gt;<br /> :Use the 'next&gt;&gt;' and 'last&gt;&gt;' links to quickly scroll through sets of 10 features.&lt;br&gt;<br /> :Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter.<br /> :Sort or reverse sort the tables using the triangle in the columns headers.<br /> :Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button.<br /> <br /> View Reactions</div>

Mkubal /w/index.php?title=SeedViewer_Organism&diff=1548 2006-11-03T19:47:47Z

<p>Mkubal: </p> <hr /> <div>Organism Page in SEED Viewer<br /> <br /> In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu&lt;br&gt;<br /> labeled 'This Organism' with the following 4 display options for this page:&lt;br&gt;<br /> <br /> Overview<br /> :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.&lt;br&gt;<br /> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.&lt;br&gt;<br /> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. <br /> :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.&lt;br&gt;<br /> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems&lt;br&gt;<br /> :present in this genome by cellular process. <br /> :At every level in the tree the number of PEGs in each category is listed in parentheses.<br /> :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. <br /> <br /> Browse Genome<br /> :This display allows you to walk the chromosome of the selected genome.&lt;br&gt;<br /> :If the genome is not completely assembled, the first contig will be selected.<br /> :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.&lt;br&gt;<br /> :The &lt; and &gt; buttons will move the window down or up the chromosome half the window size.&lt;br&gt;<br /> :The &lt;&lt; and &gt;&gt; buttons will move the window down or up the chromosome a full window size.&lt;br&gt;<br /> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.&lt;br&gt;<br /> :After selecting your options, click the 'Refresh' button to update the page.<br /> :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.&lt;br&gt;<br /> :Hover over a feature in the chromosome display for a detailed description. <br /> :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.<br /> <br /> View Features<br /> :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in base pairs relative&lt;br&gt;<br /> :to the beginning of the contig, feature type and a list of aliases.&lt;br&gt;<br /> :The total number of features for this genome is displayed above the table.&lt;br&gt;<br /> :Use the 'next&gt;&gt;' and 'last&gt;&gt;' links to quickly scroll through sets of 10 features.&lt;br&gt;<br /> :Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter.<br /> :Sort or reverse sort the tables using the triangle in the columns headers.<br /> :Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button.<br /> <br /> View Reactions</div>

Mkubal /w/index.php?title=SeedViewer_Organism&diff=1547 2006-11-03T19:46:01Z

<p>Mkubal: </p> <hr /> <div>Organism Page in SEED Viewer<br /> <br /> In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu&lt;br&gt;<br /> labeled 'This Organism' with the following 4 display options for this page:&lt;br&gt;<br /> <br /> Overview<br /> :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.&lt;br&gt;<br /> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.&lt;br&gt;<br /> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. <br /> :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.&lt;br&gt;<br /> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems&lt;br&gt;<br /> :present in this genome by cellular process. <br /> :At every level in the tree the number of PEGs in each category is listed in parentheses.<br /> :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. <br /> <br /> Browse Genome<br /> :This display allows you to walk the chromosome of the selected genome.&lt;br&gt;<br /> :If the genome is not completely assembled, the first contig will be selected.<br /> :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.&lt;br&gt;<br /> :The &lt; and &gt; buttons will move the window down or up the chromosome half the window size.&lt;br&gt;<br /> :The &lt;&lt; and &gt;&gt; buttons will move the window down or up the chromosome a full window size.&lt;br&gt;<br /> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.&lt;br&gt;<br /> :After selecting your options, click the 'Refresh' button to update the page.<br /> :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.&lt;br&gt;<br /> :Hover over a feature in the chromosome display for a detailed description. <br /> :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.<br /> <br /> View Features<br /> :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in base pairs relative&lt;br&gt;<br /> to the beginning of the contig, feature type and a list of aliases.&lt;br&gt;<br /> :The total number of features for this genome is displayed above the table.&lt;br&gt;<br /> :Use the 'next&gt;&gt;' and 'last&gt;&gt;' links to quickly scroll through sets of 10 features.&lt;br&gt;<br /> :Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then clicking enter.<br /> :Sort or reverse sort the tables using the triangle in the columns headers.<br /> :Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button.<br /> <br /> View Reactions</div>

Mkubal /w/index.php?title=SeedViewer_Organism&diff=1546 2006-11-03T16:56:34Z

<p>Mkubal: </p> <hr /> <div>Organism Page in SEED Viewer<br /> <br /> In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu&lt;br&gt;<br /> labeled 'This Organism' with the following 4 display options for this page:&lt;br&gt;<br /> <br /> Overview<br /> :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.&lt;br&gt;<br /> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.&lt;br&gt;<br /> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. <br /> :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.&lt;br&gt;<br /> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems&lt;br&gt;<br /> :present in this genome by cellular process. <br /> :At every level in the tree the number of PEGs in each category is listed in parentheses.<br /> :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. <br /> <br /> Browse Genome<br /> :This display allows you to walk the chromosome of the selected genome.&lt;br&gt;<br /> :If the genome is not completely assembled, the first contig will be selected.<br /> :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.&lt;br&gt;<br /> :The &lt; and &gt; buttons will move the window down or up the chromosome half the window size.&lt;br&gt;<br /> :The &lt;&lt; and &gt;&gt; buttons will move the window down or up the chromosome a full window size.&lt;br&gt;<br /> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.&lt;br&gt;<br /> :After selecting your options, click the 'Refresh' button to update the page.<br /> :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.&lt;br&gt;<br /> :Hover over a feature in the chromosome display for a detailed description. <br /> :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.<br /> <br /> View Features<br /> <br /> View Reactions</div>

Mkubal /w/index.php?title=SeedViewer_Organism&diff=1545 2006-11-03T16:55:31Z

<p>Mkubal: </p> <hr /> <div>Organism Page in SEED Viewer<br /> <br /> In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu&lt;br&gt;<br /> labeled 'This Organism' with the following 4 display options for this page:&lt;br&gt;<br /> <br /> Overview<br /> :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.&lt;br&gt;<br /> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.&lt;br&gt;<br /> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. <br /> :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.&lt;br&gt;<br /> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems&lt;br&gt;<br /> :present in this genome by cellular process. <br /> :At every level in the tree the number of PEGs in each category is listed in parentheses.<br /> :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. <br /> <br /> Browse Genome<br /> :This display allows a you to walk the chromosome of the selected genome.&lt;br&gt;<br /> :If the genome is not completely assembled, the first contig will be selected.<br /> :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.&lt;br&gt;<br /> :The &lt; and &gt; buttons will move the window down or up the chromosome half the window size.&lt;br&gt;<br /> :The &lt;&lt; and &gt;&gt; buttons will move the window down or up the chromosome a full window size.&lt;br&gt;<br /> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.&lt;br&gt;<br /> :After selecting your options, click the 'Refresh' button to update the page.<br /> :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.&lt;br&gt;<br /> :Hover over a feature in the chromosome display for a detailed description. <br /> :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.<br /> <br /> View Features<br /> <br /> View Reactions</div>

Mkubal /w/index.php?title=SeedViewer_Organism&diff=1544 2006-11-03T16:55:04Z

<p>Mkubal: </p> <hr /> <div>Organism Page in SEED Viewer<br /> <br /> In the green bar at the top of the page adjacent to the homepage symbol is pulldown menu&lt;br&gt;<br /> labeled 'This Organism' with the following 4 display options for this page:&lt;br&gt;<br /> <br /> Overview<br /> :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.&lt;br&gt;<br /> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.&lt;br&gt;<br /> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. <br /> :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.&lt;br&gt;<br /> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems&lt;br&gt;<br /> :present in this genome by cellular process. <br /> :At every level in the tree the number of PEGs in each category is listed in parentheses.<br /> :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. <br /> <br /> Browse Genome<br /> :This display allows a you to walk the chromosome of the selected genome.&lt;br&gt;<br /> :If the genome is not completely assembled, the first contig will be selected.<br /> :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.&lt;br&gt;<br /> :The &lt; and &gt; buttons will move the window down or up the chromosome half the window size.&lt;br&gt;<br /> :The &lt;&lt; and &gt;&gt; buttons will move the window down or up the chromosome a full window size.&lt;br&gt;<br /> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.&lt;br&gt;<br /> :After selecting your options, click the 'Refresh' button to update the page.<br /> :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.&lt;br&gt;<br /> :Hover over a feature in the chromosome display for a detailed description. <br /> :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.<br /> <br /> View Features<br /> <br /> View Reactions</div>

Mkubal /w/index.php?title=SeedViewer_Organism&diff=1543 2006-11-03T16:54:20Z

<p>Mkubal: </p> <hr /> <div>Organism Page in SEED Viewer<br /> <br /> In the green bar at the top of the page adjacent to the homepage symbol is pulldown menu&lt;br&gt;<br /> labeled 'This Organism' with the following 4 display options for this page:&lt;br&gt;<br /> <br /> Overview<br /> :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.&lt;br&gt;<br /> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.&lt;br&gt;<br /> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. <br /> :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.&lt;br&gt;<br /> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems&lt;br&gt;<br /> :present in this genome by cellular process. <br /> :At every level in the tree the number of PEGs in each category is listed in parentheses.<br /> :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. <br /> <br /> Browse Genome<br /> :This display allows a you to walk the chromosome of the selected genome.&lt;br&gt;<br /> :. If the genome is not completely assembled, the first contig will be selected.<br /> :The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.&lt;br&gt;<br /> : The &lt; and &gt; buttons will move the window down or up the chromosome half the window size.&lt;br&gt;<br /> :The &lt;&lt; and &gt;&gt; buttons will move the window down or up the chromosome a full window size.&lt;br&gt;<br /> :Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.&lt;br&gt;<br /> :After selecting your options, click the 'Refresh' button to update the page.<br /> :On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.&lt;br&gt;<br /> :Hover over a feature in the chromosome display for a detailed description. <br /> :Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.<br /> <br /> View Features<br /> <br /> View Reactions</div>

Mkubal /w/index.php?title=SeedViewer_Organism&diff=1542 2006-11-03T15:58:39Z

<p>Mkubal: </p> <hr /> <div>Organism Page in SEED Viewer<br /> <br /> In the green bar at the top of the page adjacent to the homepage symbol is pulldown menu&lt;br&gt;<br /> labeled 'This Organism' with the following 4 display options for this page:&lt;br&gt;<br /> <br /> Overview<br /> :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.&lt;br&gt;<br /> :A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.&lt;br&gt;<br /> :Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. <br /> :On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.&lt;br&gt;<br /> :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems&lt;br&gt;<br /> :present in this genome by cellular process. <br /> :At every level in the tree the number of PEGs in each category is listed in parentheses.<br /> :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. <br /> <br /> Browse Genome<br /> <br /> <br /> View Features<br /> <br /> View Reactions</div>

Mkubal /w/index.php?title=SeedViewer_HowTo&diff=1541 2006-11-02T20:30:46Z

<p>Mkubal: </p> <hr /> <div>===General Features and Conventions of SeedViewer===<br /> :Tool tips - [?] indicates a tool tip will appear when hovered above with the mouse. Underlined [?] indicates a clickable tool tip &lt;br&gt;<br /> :that also links into a wiki page for a more detailed explanation<br /> <br /> :Text Entry Boxes - if the text box has a pulldown menu beneath it, as text is entered in the box the menu will be updated with only items&lt;br&gt;<br /> :that match or contain the entered text.<br /> <br /> :Sorting Table Entries - alpahnumerically sort or reverse sort with the respective triangle in a column header<br /> <br /> :Browsing Table Entries - use the next&gt;&gt; and last&gt;&gt; links to quickly browse tables with more than 10 rows <br /> <br /> ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:===<br /> <br /> :[[SeedViewer_Home| Home page]]<br /> <br /> :[[SeedViewer_Organism| Organism page]]<br /> <br /> :[[SeedViewer_Search| Annotation page]]<br /> <br /> :[[SeedViewer_Functional_Role| Functional Role page]]<br /> <br /> :[[SeedViewer_Subsystem| Subsystem page]]<br /> <br /> ===For tutorials on accomplishing specific tasks, please follow the link below:===<br /> <br /> :[[SeedViewer_Tutorial| Tutorials]]</div>

Mkubal /w/index.php?title=SeedViewer_HowTo&diff=1540 2006-11-02T20:29:42Z

<p>Mkubal: </p> <hr /> <div>===General Features and Conventions of SeedViewer===<br /> :Tool tips - [?] indicates a tool tip will appear when hovered above with the mouse. Underlined [?] indicates a clickable tool tip &lt;br&gt;<br /> :that also links into a wiki page for a more detailed explanation&lt;br&gt;<br /> :Text Entry Boxes - if the text box has a pulldown menu beneath it, as text is entered in the box the menu will be updated with only items&lt;br&gt;<br /> that match or contain the entered text.&lt;br&gt;<br /> :Sorting Table Entries - alpahnumerically sort or reverse sort with the respective triangle in a column header&lt;br&gt;<br /> :Browsing Table Entries - use the next&gt;&gt; and last&gt;&gt; links to quickly browse tables with more than 10 rows <br /> <br /> ===For a description of how to use the features on the different Seed Viewer pages, please follow the links below:===<br /> <br /> :[[SeedViewer_Home| Home page]]<br /> <br /> :[[SeedViewer_Organism| Organism page]]<br /> <br /> :[[SeedViewer_Search| Annotation page]]<br /> <br /> :[[SeedViewer_Functional_Role| Functional Role page]]<br /> <br /> :[[SeedViewer_Subsystem| Subsystem page]]<br /> <br /> ===For tutorials on accomplishing specific tasks, please follow the link below:===<br /> <br /> :[[SeedViewer_Tutorial| Tutorials]]</div>

Mkubal /w/index.php?title=SeedViewer_Home&diff=1539 2006-11-02T20:06:50Z

<p>Mkubal: </p> <hr /> <div>===Counts of Genomes in the SEED===<br /> <br /> The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.&lt;br&gt;<br /> A box on the top right of the home page provides a current total and complete count of each type.<br /> <br /> ===Searching===<br /> <br /> The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.&lt;br&gt;<br /> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.&lt;br&gt;<br /> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives.<br /> <br /> Text Search&lt;br&gt;<br /> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.&lt;br&gt;<br /> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features.<br /> :The results of the search will be displayed in up to 3 tables, a Functional Role table, Subsystem table and Features table.&lt;br&gt;<br /> :The number of hits associated with a functional role will appear above the Functional Role table. &lt;br&gt;<br /> :The number of features returned is limited to 100. &lt;br&gt;<br /> :To browse the results quickly use the next &gt;&gt; and last &gt;&gt; links. <br /> :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.&lt;br&gt;<br /> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem.<br /> :In any of the results tables,<br /> :clicking on a functional role will take you to a Functional Role page in the SEED Viewer,<br /> :clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and<br /> :clicking on a PEG ID will take you an Annotation page in the SEED Viewer.<br /> <br /> Blast Search&lt;br&gt;<br /> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.&lt;br&gt;<br /> : Then click the 'Blast Search' button to the right of the genome pulldown menu. <br /> : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer.<br /> <br /> Subsystems Search&lt;br&gt;<br /> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the subsystem name.<br /> :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer.<br /> <br /> Organism Search&lt;br&gt;<br /> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the genome.<br /> :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer.</div>

Mkubal /w/index.php?title=SeedViewer_Home&diff=1538 2006-11-02T19:59:42Z

<p>Mkubal: </p> <hr /> <div>===Counts of Genomes in the SEED===<br /> <br /> The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.&lt;br&gt;<br /> A box on the top right of the home page provides a current total and complete count of each type.<br /> <br /> ===Searching===<br /> <br /> The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.&lt;br&gt;<br /> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change the search perspective.&lt;br&gt;<br /> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives.<br /> <br /> Text Search&lt;br&gt;<br /> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.&lt;br&gt;<br /> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features.<br /> :The results of the search will be displayed in up to 3 tables, a Functional Role table, Subsystem table and Features table.&lt;br&gt;<br /> :The number of hits associated with a functional role will appear above the Functional Role table. &lt;br&gt;<br /> :The number of features returned is limited to 100. &lt;br&gt;<br /> :To browse the results quickly use the next &gt;&gt; and last &gt;&gt; links. <br /> :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.&lt;br&gt;<br /> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem.<br /> <br /> Blast Search&lt;br&gt;<br /> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.&lt;br&gt;<br /> : Then click the 'Blast Search' button to the right of the genome pulldown menu. <br /> : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer.<br /> <br /> Subsystems Search&lt;br&gt;<br /> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the subsystem name.<br /> :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer.<br /> <br /> Organism Search&lt;br&gt;<br /> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the genome.<br /> :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer.</div>

Mkubal /w/index.php?title=SeedViewer_Home&diff=1537 2006-11-02T19:58:44Z

<p>Mkubal: </p> <hr /> <div>===Counts of Genomes in the SEED===<br /> <br /> The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.&lt;br&gt;<br /> A box on the top right of the home page provides a current total and complete count of each type.<br /> <br /> ===Searching===<br /> <br /> The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.&lt;br&gt;<br /> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.&lt;br&gt;<br /> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives.<br /> <br /> Text Search&lt;br&gt;<br /> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.&lt;br&gt;<br /> :The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features.<br /> :The results of the search will be displayed in up to 3 tables, a Functional Role table, Subsystem table and Features table.&lt;br&gt;<br /> :The number of hits associated with a functional role will appear above the Functional Role table. &lt;br&gt;<br /> :The number of features returned is limited to 100. &lt;br&gt;<br /> :To browse the results quickly use the next &gt;&gt; and last &gt;&gt; links. <br /> :The columns in all tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in a column header.&lt;br&gt;<br /> :If you check the 'quick search' option, the results will be limited to functionals role in a subsystem.<br /> <br /> Blast Search&lt;br&gt;<br /> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.&lt;br&gt;<br /> : Then click the 'Blast Search' button to the right of the genome pulldown menu. <br /> : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer.<br /> <br /> Subsystems Search&lt;br&gt;<br /> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the subsystem name.<br /> :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer.<br /> <br /> Organism Search&lt;br&gt;<br /> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the genome.<br /> :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer.</div>

Mkubal /w/index.php?title=SeedViewer_Home&diff=1536 2006-11-02T19:37:21Z

<p>Mkubal: </p> <hr /> <div>===Counts of Genomes in the SEED===<br /> <br /> The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.&lt;br&gt;<br /> A box on the top right of the home page provides a current total and complete count of each type.<br /> <br /> ===Searching===<br /> <br /> The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.&lt;br&gt;<br /> By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.&lt;br&gt;<br /> Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives.<br /> <br /> Text Search&lt;br&gt;<br /> :This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.&lt;br&gt;<br /> :This search cover features, functional roles and subsystems.<br /> :If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem.<br /> :The results of the search will be displayed in 2 tables, a Functional Role table and Subsystem table. The number of hits associated &lt;br&gt;<br /> :with a functional role will appear above the Functional Role table. To browse the results quickly use the next &gt;&gt; and last &gt;&gt; links. <br /> :The columns in both tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in the column header.&lt;br&gt;<br /> <br /> Blast Search&lt;br&gt;<br /> : Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.&lt;br&gt;<br /> : Then click the 'Blast Search' button to the right of the genome pulldown menu. <br /> : The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer.<br /> <br /> Subsystems Search&lt;br&gt;<br /> :Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the subsystem name.<br /> :After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer.<br /> <br /> Organism Search&lt;br&gt;<br /> :Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.&lt;br&gt;<br /> :Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,&lt;br&gt;<br /> :and not just matching at the beginning of the genome.<br /> :After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer.</div>

Mkubal