https:/// /w/index.php?title=Special:NewPages&feed=atom&hideredirs=1&limit=50&offset=&namespace=0&username=&tagfilter=TheSeed - New pages [en]2024-03-29T08:34:07ZFrom TheSeedMediaWiki 1.35.6 /wiki/FIGfams/FIGfams/2009-04-27T18:13:50Z<p>FolkerMeyer: </p>
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<div>This is the new home of the FIGfams (ALEX is going to make it that)</div>FolkerMeyer /wiki/AnnotationClearingHouseAnnotationClearingHouse2008-12-15T11:55:35Z<p>DanielaBartels: </p>
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<div>== Annotation Clearing House ==</div>DanielaBartels /wiki/SEED_Viewer_Manual/IMGMAPTESTSEED Viewer Manual/IMGMAPTEST2008-12-12T10:20:41Z<p>DanielaBartels: </p>
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<div><img src="http://www.theseed.org/w/images/0/04/ContigView1.png" usemap="#map" /><br />
<br />
<map name='map'><br />
<area shape='rect' coords='230,36,367,58' href='www.google.de' /><br />
</map></div>DanielaBartels /wiki/WebComponents/ListSelectWebComponents/ListSelect2008-12-08T13:39:35Z<p>DanielaBartels: /* List Select */</p>
<hr />
<div>== List Select ==<br />
<br />
This Component is used to select a number of items from a list. Usually, it is bound to a table where it adds additional columns from the list.<br />
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To select an item to add, mark the item and then the right arrow to put it into the right list. To remove it, mark it in the right list and click the left button to put it back.<br />
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The table the list select is bound to should update automatically.<br />
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[[Image:ListSelect.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/Editing_Capabilities/ChromosomalClustersSEED Viewer Manual/Editing Capabilities/ChromosomalClusters2008-12-05T17:01:56Z<p>DanielaBartels: /* Details table */</p>
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<div>== Editing Capabilities - Chromosomal Clusters ==<br />
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This page can be accessed from a [[SEED_Viewer_Manual/Annotation#Chromosomal Clusters|Chromosomal Clusters]] view, using the button '''annotate clusters''' (only visible if you have editing rights for the genome).<br />
<br />
=== Overview Table ===<br />
<br />
The first table on the page lists all sets of protein visible in the Chromosomal Clusters view. The set numbers in the first column are the set numbers from the view. The second column ('''#features''') shows the number of features in the set. '''#functions''' depicts how many different functions the features in the set have. One of the functions is displayed in the column '''first function'''. Whenever there is more than one function, the cell in the next column will be painted in red, as it is not '''consistent''', else green. With the check boxes in the last column, you can turn on and off the details tables for each of the sets.<br />
<br />
Above the table, there are four buttons to turn on/off the details tables. '''show all''' will remove previous filtering and show you all details tables again. '''show none''' will remove all details tables, so that you can afterwards select single ones you'd like to see. '''show consistenct''' and '''show inconsistent''' is related to the '''consistent''' column in the table. It will display the details tables with a consistent or an inconsistent set, respectively.<br />
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[[Image:Chromosomal1.png]]<br />
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=== Details table ===<br />
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As a default, for each set you will get a details table in the following. These list all the features in the set. The set number is displayed in the first column. '''Organism''' is the genome the feature stems from. If there are more than one occurrence of features in the set for one genome, they are numbered in the '''Occ''' column. If there is a [http://www.uniprot.org UniProt] alias for the feature, the ID and the function of this alias will be shown in the next two columns. <br />
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The IDs of the features in the next column '''Feature''' link to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. If the feature is in a subsystem, you will find one or many (comma-separated) numbers in the '''SS''' column. Hovering over the cell will display a tooltip with the names of the subsystems. The column '''Ev''' shows Evidence Codes for the feature. There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].<br />
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The length of the feature is shown in the next column ('''Ln'''). Its current function can be found in the column '''Function'''. Same colors in this column indicate same functions. Links to a [[SEED_Viewer_Manual/FIGfamViewer|FIGfam]] a feature is member of are displayed in the last column.<br />
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Editing the function for the features in the Details table is done by checking a function or entering a new one, then clicking the '''annotate''' button. You can select a UniProt function, or one of the other feature's functions. If you want to use a new one, enter it in the '''new function''' text field and check the radio box next to it. The new function will be used to annotate all features that are checked in the '''Feature''' column. You will only be able to check features you can edit. In this example, only the ''Escherichia coli K12'' can be edited, so you will find a checkbox only for this feature.<br />
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To align features in the [[SEED_Viewer_Manual/AlignSeqs|Alignment Page]], check the features of interest and press the button '''align'''.<br />
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The buttons '''check all''', '''uncheck all''' and '''check to last checked''' can be used for the check boxes of the features, which is especially important for large tables.<br />
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[[Image:Chromosomal2.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/Editing_Capabilities/CreateFeatureSEED Viewer Manual/Editing Capabilities/CreateFeature2008-12-05T13:23:03Z<p>DanielaBartels: /* Actions panel */</p>
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<div>== Editing Capabilities - Create Feature ==<br />
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This page lets you create a new protein feature. It consists of three parts, a Control [[WebComponents/Tabview|TabView]], an '''Actions''' panel and the '''Sequence Table'''.<br />
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=== Control TabView ===<br />
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In the first tab of this TabView, you can put in a function for your newly created feature by just entering it into the text field.<br />
Below that, you can see two text fields for controlling ''Up/Downstream Nucleotides'''. As you usually enter this page from the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]], you have a hit region defined in which the feature is to be located. The numbers you can enter are the number of upstream and downstream nucleotides of the hit you want to see in the '''Sequence Table'''. After entering your numbers, click the '''update''' button in the '''Actions''' panel<br />
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The second tab of the TabView lists all codons of the genetic code. Here, you can select the start codons that are possible for the genome you want to create a feature in. Pre-selected are the standard start codons that are usually used for bacterial genomes. You can choose a different set of codons and press the button '''update''' in the '''Actions''' panel to change the view in the '''Sequence Table'''. <br />
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The genetic code can have small differences from the default genetic code in some organisms. You can change the standard genetic code in the third tab of the TabView. For each triplet, you can see the default amino acid that is usually used in organisms. If you want to change this for a triplet, click the respective drop down box and choose the right amino acid. To make the changes visible in the '''Sequence Table''', press the '''update''' button in the '''Actions''' panel again.<br />
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[[Image:CNFTab.png]]<br />
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=== Actions panel ===<br />
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The actions panel consists of three buttons. The '''update''' will let you update the '''Sequence Table''' with new parameters you can type in the '''Control TabView'''. <br />
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Clicking the second button, '''blastp''' will perform a protein based BLAST of the region selected in the '''Sequence Table'''. For this, you have to choose a '''start'''codon in the table. The sequence taken for the BLAST comparison is the translated protein sequence of the region from that start codon to the next stop codon in that frame. Note that you do not select a '''stop''' codon. If you select a '''stop''' codon, this will be ignored for defining the sequence region.<br />
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The blast search will result in a [[WebComponents/Table|table]] with all hit proteins. The table shows the hit feature and it's function. You can select a function in this table for the new protein you want to create, instead of putting in a new on in the '''Control TabView''' above.<br />
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If you have selected a '''start''' codon in the '''Sequence Table''', you can also directly create the feature for that region if you are sure about it. Clicking the '''create''' button will do that.<br />
<br />
[[Image:CNFActions.png]]<br />
<br />
=== Sequence Table ===<br />
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The sequence table is a table of the codons in a genomic region. Each cell represents a triplet. The first line of each line is the translation of that triplet to amino acid. A ''*'' stands for a '''stop''' codon. The second line shows the actual triplet (the codon). <br />
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The third line can have dots (...), forward arrows (>>>) or reverse arrows (<<<). Dots mean that there not feature overlaps this part of the region. Forward arrows represent a feature on the forward strand, reverse arrows on the reverse strand. This way, you can see if the feature you want to create overlaps with an already present feature in that region. <br />
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The fourth line sometimes has a check box or a radio box. Radio boxes are shown for every '''start''' codon. A cell with a start codon is also painted in a green color. Check a radio box to mark the start of the feature. RBS binding sites (purple colored cells) can help to determine the right start codon. Check boxes are used for '''stop''' codons (cells with red color). Check the check box of a '''stop''' codon to ignore it, meaning that the feature be continue to the next (unchecked) '''stop''' codon. <br />
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[[Image:CreateNewFeature.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/Editing_Capabilities/SearchGeneSEED Viewer Manual/Editing Capabilities/SearchGene2008-12-05T11:03:36Z<p>DanielaBartels: /* Editing Capabilities - Search Gene Page */</p>
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<div>== Editing Capabilities - Search Gene Page ==<br />
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If you have the right to edit the genome for which the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]] is displayed, you will additional options to '''annotate a found feature''' or '''create a new feature'''.<br />
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=== Annotate a found feature ===<br />
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The BLAST [[WebComponents/Table|table]] now has an additional column on the left to check the hit feature. If you click the newly appeared button '''Assign Role''', you will annotate the hit feature with the function of the matched feature.<br />
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The arrows in the graphics in the '''Is the gene maybe not called?''' section are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] where you will also have the option to annotate the feature if you have the right to [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|edit the feature]].<br />
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=== Create new feature ===<br />
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If you have found a missing feature in the tblastn graphics, you can click the hit (marked by a ''Q'') to get to the [[SEED_Viewer_Manual/Editing_Capabilities/CreateFeature|Create Feature]] page.</div>DanielaBartels /wiki/SEED_Viewer_Manual/AlignSeqsSEED Viewer Manual/AlignSeqs2008-12-05T10:33:51Z<p>DanielaBartels: /* Align Sequences */</p>
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<div>== Align Sequences ==<br />
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This page is usually loaded if you have selected a number of features in e.g. the [[SEED_Viewer_Manual/Evidence|Evidence Page]] and pressed an '''Align Sequences''' button. Here, the alignment is presented. The alignment software that is used is [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html T-Coffee], a method for fast and accurate multiple sequence alignment.<br />
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On the top of the alignment, you can see a color legend for aligned regions. Below, the multiple alignment for all chosen features is displayed.<br />
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[[Image:AlignSeqs.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/Editing_Capabilities/EvidenceSEED Viewer Manual/Editing Capabilities/Evidence2008-12-05T09:21:18Z<p>DanielaBartels: /* Editing Capabilities - Evidence Page */</p>
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<div>== Editing Capabilities - Evidence Page ==<br />
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If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Evidence|Evidence Page]] is displayed, there will be some additional options visible in the ''[[SEED_Viewer_Manual/Evidence#Tabular Protein Evidence|Tabular Protein Evidence tab]]''.<br />
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The fields to enter a new function are the same as in the [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Editing capability in the Annotation Page]]. The new function is assigned to all selected features in the table below the fields (use the checkboxes in the first column of the [[WebComponents/Table|table]]). If you have entered a new function, press '''Assign Function''' to annotate the selected features.<br />
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To assign the selected features with an already existing function from the table, select the feature assigned with the function with the radio box in the rightmost column of the table, and leave the text fields above empty. Again, use the '''Assign Function''' button to make your annotations.<br />
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[[Image:EditEvidence1.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/EditLiteratureSEED Viewer Manual/EditLiterature2008-12-04T15:35:21Z<p>DanielaBartels: /* Curating literature in SEED */</p>
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<div>== Edit Literature ==<br />
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This page allows you to edit direct literature (dlits) for a feature. The tool automatically queries PubMed for Aliases of the feature ID to get candidate literatures for your feature.<br />
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=== CDS Info ===<br />
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This section displays a table with general information for the feature that might be valuable for deciding if a literature reference is relevant for the feature. <br />
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=== Requesting relevant publications from PubMed ===<br />
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This section displays publications that are not yet curated, as well as publications that are already assigned to be relevant or not relevant to the function of the feature. The literature references appear in the following tables:<br />
<br />
'''Not yet Curated relevant publications:'''<br />
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These are publications the tool has identified as possibly relevant for the feature. You will get a checkbox in the first column of the table. Check the publications you want to assign as supporting the functional assignment of the feature, and press the button '''Save to relevant pmids''' underneath the table to save them as dlits.<br />
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'''Not yet curated publications (dlits):''' <br />
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Same as above, but the literature references were pre-computed.<br />
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'''Current DLITS for this gene:'''<br />
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This table shows all publications that are assigned to support the functional assignment of the feature (to be dlits).<br />
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'''Curated to be RELEVANT, but NOT DLITS:'''<br />
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Literature that is relevant, but not a dlit is literature that does not support the functional assignment to the feature, but refer to the genomic region the feature is in or give other information about the feature.<br />
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'''Curated to be GENOME PAPERS, not dlits:'''<br />
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These are references that refer to the whole genome of the feature or a genomic region, not directly the feature itself. Mostly, these papers deal with the sequencing process of the genome.<br />
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'''Curated to be NOT RELEVANT publications:'''<br />
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Not relevant publications.<br />
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=== Curating literature in SEED ===<br />
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Curation of the literature can be done two ways:<br />
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'''1) Add additional publications for this peg'''<br />
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You can manually add publications that have not appeared in any of the tables above. If you want to add more than one PubMed reference, separate them with a space. Press '''Save to relevant pmids''' to save the entered publications as supporting the functional assignment of the feature (dlit).<br />
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'''2) Drag and drop the PMID to the appropriate containers.'''<br />
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The categories for the publications described above can be found as containers in this section. The literature boxes in the containsers can be dragged and dropped from one container to another. This way, you can move any of the literature references to any container. If you have made your selection, press '''Save to attributes''' to save your selection.</div>DanielaBartels /wiki/SEED_Viewer_Manual/Editing_Capabilities/AnnotationSEED Viewer Manual/Editing Capabilities/Annotation2008-12-04T14:42:05Z<p>DanielaBartels: /* Editing Capabilities - Annotation Page */</p>
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<div>== Editing Capabilities - Annotation Page ==<br />
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If you have the right to edit the feature for which the [[SEED_Viewer_Manual/Annotation|Annotation Page]] is displayed, you will get two additional fields in the Annotation Overview, '''new assignment''' and '''comment'''. <br />
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To annotate a feature, you can simply put the new assignment into the text field at the '''new assignment'''. Note that the annotation can be a combination of functional roles. Functional roles can be combined to an assignment using different separators:<br />
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' / ' separates two functional roles that refer to different parts of the feature. This separator is for example used for fusion genes, or multi-domain proteins where different domains implement those functional roles. <br />
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' @ ' also separates different functional roles for one protein, but the functions refer to the same part of the protein. This is used if a domain or a part of the protein can implement both functions in different contexts.<br />
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' ; ' is used if you are unsure which of the functions a protein implements. <br />
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' # ' is followed by a text that is added as a comment to the functional role. This is for example used for marking features as truncated.<br />
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If you'd like to give additional comments to your annotation, the '''comment''' textbox is the right place for this. After typing in your new functional assignment to your feature, press '''change''' to make the annotation. <br />
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Another option that you have access to if you can edit the feature is deleting it. If you are sure that the feature should be deleted, press the button '''delete feature'''. The system will ask you again if you really want to delete the feature, to prevent people from accidently deleting features.<br />
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'''curate literature''' leads to a page where you can add direct literature links (dlits) to a feature. Press [[SEED_Viewer_Manual/EditLiterature|here]] to get more information.<br />
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[[Image:AnnotationEdit.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/RequestNewPasswordSEED Viewer Manual/RequestNewPassword2008-12-04T11:08:48Z<p>DanielaBartels: /* Request New Password */</p>
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<div>== Request New Password ==<br />
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If you have a login, but you forgot your password, you can use this page to get a new one. Type in your user login and your email address, and press the button '''Request new password'''. The system will check if your login fits to your email (meaning that you have to use the same email as you did when requesting the account). It will then send you a new cryptic password, which you should immediately change using the [[SEED_Viewer_Manual/UserManagement|User Management]] link (for more information see [[WebComponents/Login|here]]).<br />
<br />
If you cannot access your email any more, you have to contact the SEED team using the '''Contact''' link in the '''[[SEED_Viewer_Manual/Menu#Help Menu|Help Menu]]''' for help.<br />
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[[Image:RequestPassword.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/FIGfamsReleaseSEED Viewer Manual/FIGfamsRelease2008-12-04T10:42:24Z<p>DanielaBartels: /* FIGfams Release */</p>
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<div>== FIGfams Release ==<br />
<br />
Here you can find some statistics about FIGfams presented in a [[WebComponents/Tabview|TabView]]. The different tabs show you information about the '''Size Distribution''', the '''Subsystem Coverage''' and '''Quality Control''' of the FIGfams.<br />
<br />
=== Size Distribution ===<br />
<br />
This tab shows a graphic displaying the FIGfam Size against the FIGfam Quantity, for all releases of the FIGfams. For the latest release, you get a little table that tells you about the '''Version''', the '''Date''' the release was done, the number of FIGfams ('''FIGfams Quantity''') and the total number of sequences in FIGfams ('''Total Sequences''').<br />
<br />
=== Subsystem Coverage ===<br />
<br />
The left bar in the graphics on this tab shows you the '''Subsystem Coverage''' of the FIGfams, meaning what percentage of the FIGfams is covered by subsystems. For these, you see a '''Category Distribution''' in the piechart in the middle. The tree right to the piechart lets you browse the categories shown in the piechart. For additional information how the use the graphics, see a similar graphic on the [[SEED_Viewer_Manual/OrganismPage#Subsystem Information|OrganismPage]].<br />
<br />
=== Quality Control ===<br />
<br />
The third tab explains how Quality Control is made for the FIGfams using a small set of genomes. These are annotated using the FIGfams, and the annotations are compared against the current annotations of the genomes.</div>DanielaBartels /wiki/SEED_Viewer_Manual/FIGfamsSEED Viewer Manual/FIGfams2008-12-03T18:34:24Z<p>DanielaBartels: /* FIGfams Page */</p>
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<div>== FIGfams Page ==<br />
<br />
This page explains a lot about FIGfams in the text. You can also find a link to the version history and some statistics using the link '''history and statistics'''.<br />
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On the right side of the page you can find two ways of accessing the FIGfams. The first text box under '''Enter FIGfam, Keyword or a sequence FIG id''' lets you enter a search text. Click return to get the result.<br />
<br />
[[Image:FIGfamsSearch1.png]]<br />
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The result of the search is a three-column table with hits. The '''FIGfam ID''' links to the [[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer Page]] for the FIGfam hit. The '''Function''' is the functional role assigned to the FIGfam. The number of sequences that belong to the FIGfam is displayed in the column '''Sequence Quantity'''.<br />
<br />
[[Image:FIGfamsResult1.png]]<br />
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The second search you can do is paste a fasta sequence into the second text field under '''Or scan a fasta sequence against the FIGfams'''. Press the button '''search''' to get the results.<br />
<br />
[[Image:FIGfamsSearch3.png]]<br />
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In this case, you will find the best hit of your sequence against the FIGfams. The '''Hit family''' links to the [[SEED_Viewer_Manual/FIGfamViewer|FIGfam Viewer Page]] of the FIGfam. <br />
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[[Image:FIGfamsResult2.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/FIGfamViewerSEED Viewer Manual/FIGfamViewer2008-12-03T18:32:36Z<p>DanielaBartels: /* FIGfam Viewer */</p>
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<div>== FIGfam Viewer ==<br />
<br />
The table on the top of the page displays the '''FIGfam ID''' and the '''Functional Role''' associated to the FIGfam. Subsystems that are associated with members of the FIGfam are displayed in the third row ('''Subsystems''') of the table. They are linked to the [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] of the subsystem. The '''FIGfam Size''' is the number of members of the FIGfam. The '''Average Sequence Length''' is the medium of aminoacids sequence length of the members of the FIGfam. Behind this there is a short statistics telling you the member with the '''Maximum length''', '''Minimum length''' and the '''Standard Deviation'''.<br />
<br />
The '''Member list''' is a [[WebComponents/Table|table]] showing the '''ID''' of the member (the link leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]), the '''Organism''' it belongs to, '''Associated Subsystem''' (there can be more than one) and the function of the member. You can export the list in ''tab-separated format'' using the '''export table''' button. For downloading a fasta file of the protein sequences of the members, press the '''Fasta''' button on the left.<br />
<br />
[[Image:FIGfamViewerTable.png]]<br />
<br />
The bottom part of the page shows a '''Compare Regions View''' of the members of the FIGfam. The right graphics is a '''Compare Regions''' just like the one on the [[SEED_Viewer_Manual/Annotation|Annotation Page]]. Click [[SEED_Viewer_Manual/Annotation#Compare Regions|here]] to get a learn more.<br />
<br />
The left part is used to filter the Compare Regions View. It is an phylogenetic tree showing only the phyla with members for the FIGfam. Click the '''+''' signs to expand and '''-''' signs to collapse a part. You can deselect check boxes to remove the organisms from the Compare Regions View. Press '''Refresh Context''' to update the View.<br />
<br />
If you want to find a member of the FIGfam, you can put the ID into the text field on top of the tree. Clicking the '''search in tree''' button will expand the tree up to the position of the FIGfam member.<br />
<br />
The button '''get selected fasta''' will let you download the fasta sequences of all members in the organisms you have selected in the tree. <br />
<br />
[[Image:FIGfamViewerTree.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/ScenariosSEED Viewer Manual/Scenarios2008-12-03T16:45:40Z<p>DanielaBartels: /* Scenarios */</p>
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<div>== Scenarios ==<br />
<br />
[[Glossary#Scenarios|Scenarios]] are components of a metabolic reaction network in which specific compounds are labeled as inputs and outputs.<br />
The [[WebComponents/Table|table]] on this page lists all Scenarios. You can select a number of genomes to find out which scenarios are present for these organisms.<br />
<br />
To choose the organisms of interest, you can click the button '''select organisms'''. It will open a [[WebComponents/ListSelect|List Select]] that contains all organisms you can choose from. Select an organism and press the right arrow. The organism will appear in the right box and the table will be updated. An additional column will appear for the chosen organism.<br />
<br />
[[Image:Scenarios1.png]]<br />
<br />
As a scenario is bound to a SEED [[Glossary#Subsystem|subsystem]], the first three columns show the classification ('''Category''' and '''Subcategory''') and the name of the '''Subsystem'''. The subsystem name links to its [[SEED_Viewer_Manual/Subsystems|Subsystem]] page. The name of the '''Scenario''' is displayed in the fourth column. The [http://www.genome.jp/kegg/ KEGG] map for the scenario is shown in the next column. Following columns tell you for each chosen genome if the scenario is implemented in the organism. <br />
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[[Image:Scenarios2.png]]</div>DanielaBartels /wiki/WebComponents/FilterSelectWebComponents/FilterSelect2008-12-03T15:19:07Z<p>DanielaBartels: /* Filter Select */</p>
<hr />
<div>== Filter Select ==<br />
<br />
A '''Filter Select''' contains two components: a Text Box and a Select Box. The Select Box contains all options the user can select. Use the scroll bar on the right to browse through the options. If a Select Box is a ''multiple'' Select Box, you can select more than one option. <br />
<br />
Searching for an option can be done using the Text Box on top of the Select Box. If you start typing, the Filter Select will automatically remove all options that do not fit to the keyword, meaning that an infix search is done on the options and not-matching options are removed.<br />
<br />
In the example, you see a [http://www.genome.jp/kegg/ KEGG] map select you can find on the [[SEED_Viewer_Manual/KEGG|KEGG Page]] of the [[SEED_Viewer_Manual|SeedViewer]]. This Filter Select is not multiple, so that you can only choose one KEGG map from the list.<br />
<br />
[[Image:KeggMapSelect.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/KEGGSEED Viewer Manual/KEGG2008-12-03T14:28:42Z<p>DanielaBartels: /* Kegg Maps */</p>
<hr />
<div>== Kegg Maps ==<br />
<br />
This page allows you to view [http://www.genome.jp/kegg/ KEGG] maps and statistics for chosen organisms in the SEED. <br />
<br />
Usually, you enter this page from a page that had an organism defined. The chosen organism is stated in the header:<br />
<br />
[[Image:KeggMapHeader.png]]<br />
<br />
Entering the page, you will see the overview [http://www.genome.jp/kegg/ KEGG] map pre-selected, which is '''Metabolism'''.<br />
In the following [[WebComponents/FilterSelect|Filter Select]] you can select another map. Press '''select''' to display the map in the graphic on the bottom of the page.<br />
<br />
[[Image:KeggMapSelect.png]]<br />
<br />
In the example, the [http://www.genome.jp/kegg/ KEGG] map '''Lysine Biosynthesis''' was selected. The map shows the connections between the enzymes and the educts / products of the reactions the enzymes perform. <br />
<br />
The enzyme numbers (EC-Numbers) are connected to features in SEED organisms through the [[Glossary#Functional Role|functional role]] assignments to the features. The map is colored for the chosen organism (in this case ''Escherichia coli K12''). If the organism implements a functional role with the EC-number in the map, its box is colored in green, else white.<br />
<br />
The blue boxes in the map link to neighboring (connected) maps in the metabolism.<br />
<br />
[[Image:KeggMap.png]]<br />
<br />
You can view statistics for up to four additional organisms compared to the chosen organism. Select these organisms in the [[WebComponents/ListSelect|List Select]] top right on the page. Choose an organism and press the ''right arrow'' to select it. For unselecting it, choose it in the right box and press the ''left arrow''. After making your selection, press the '''select''' button on the left (same button as above).<br />
<br />
[[Image:KeggOrgSelect.png]]<br />
<br />
The statistics table will show all connecting maps of the selected category for your organisms. For each map, you can see the number of implemented EC-numbers in each organism, as well as the percent of total EC-numbers that are implemented as a green bar. The number links to the connecting map for the organism.<br />
<br />
[[Image:KeggOrgTable.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/ContigViewSEED Viewer Manual/ContigView2008-12-02T16:46:42Z<p>DanielaBartels: /* Contig View */</p>
<hr />
<div>== Contig View ==<br />
<br />
This page shows a window of the Contig centered on a selected feature. The window is described in the top table. It names the '''Organism''' and '''Contig Length''' for the feature. The '''Start Base''' and '''End Base''' of the window and the resulting '''Region Length''' is shown. The '''Region GC Content''' is computed for that window.<br />
<br />
For the selected feature, the second table gives you the Protein ID ('''Protein of Interest Region'''), the '''Contig''' name, as well as the '''Start Codon Location''' and the '''Stop Codon Location'''.<br />
<br />
[[Image:ContigView1.png]]<br />
<br />
The graphic displays the window in a six-frame view. You can use the horizontal scroll bar to navigate the window. <br />
<br />
The DNA sequence for both strands is displayed in small colored letters. The four bases are colored as follows: ''t'' - blue, ''c'' - red, ''a'' - purple and ''g'' - green. Background colors are used to mark possible '''Start Codons''' (yellow) and '''Shine-Dalgarno sites''' (green).<br />
<br />
Above the forward strand DNA sequence, you can see the translated protein sequences for the three forward strands. A ''*'' marks a stop codon. Below the reverse-strand DNA sequence, the three reverse protein strands are shown. Protein features are displayed in form of boxes on the respective strand. The selected feature ('''Protein of interest''') gets a box with a red background, other features have a box with blue background. <br />
<br />
Below the six-frame view, you can find a '''Third GC Codon plot'''. The dotted line is the average GC content for the region. The colored lines are the GC content for the third Codon of the triplets for each strand.<br />
<br />
[[Image:ContigView2.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/Editing_CapabilitiesSEED Viewer Manual/Editing Capabilities2008-12-02T16:23:23Z<p>DanielaBartels: /* Editing capabilities in the SeedViewer */</p>
<hr />
<div>== Editing capabilities in the SeedViewer ==<br />
<br />
[[SEED_Viewer_Manual/Editing_Capabilities/Annotation|Annotation Page]]<br />
<br />
[[SEED_Viewer_Manual/Editing_Capabilities/ChromosomalClusters|Chromosomal Clusters Page]]<br />
<br />
[[SEED_Viewer_Manual/Editing_Capabilities/Evidence|Evidence Page]]<br />
<br />
[[SEED_Viewer_Manual/Editing_Capabilities/SearchGene|Search Gene Page]]<br />
<br />
[[SEED_Viewer_Manual/Editing_Capabilities/CreateFeature|Create new Feature Page]]<br />
<br />
[[SEED_Viewer_Manual/EditLiterature|Edit Literature for a feature]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/SearchGeneSEED Viewer Manual/SearchGene2008-12-02T14:56:05Z<p>DanielaBartels: /* Search Gene */</p>
<hr />
<div>== Search Gene ==<br />
<br />
In this page you can search for a function in a genome in the context of a subsystem. Two ways of looking for a candidate feature for the function are provided: Looking for already existing features in the genome using a protein-based BLAST search, and trying to find candidates via a translated BLAST search against the DNA sequence of the whole genome. In both cases, '''reference feature(s)''' are selected (or given to the page) from already existing features with assigned with the functional role that are part of the given subsystem.<br />
<br />
If you are logged in and you have the right to annotate the genome, you will see additional annotation capabilities on this page (described [[SEED_Viewer_Manual/Editing_Capabilities/SearchGene|here]]).<br />
<br />
=== Candidate genes found by Similarity (BLAST)? ===<br />
<br />
This part looks for [[Glossary#Similarities|Similarities]] of all '''reference feature''' (features in the subsystem that are assigned with the function) to the features of the selected genome. The output [[WebComponents/Table|table]] lists the E-Value ('''P-Sc'''), the reference feature that was hit ('''PEG'''), the length ('''Len''') of the hit feature, the current function of the hit feature ('''Current fn'''), as well as the query feature ('''Matched peg'''), its length ('''Len'''), and its '''Function'''.<br />
<br />
[[Image:SearchGene1.png]]<br />
<br />
=== Is the gene maybe not called? ===<br />
<br />
In this case, a '''reference feature''' is used for a translated BLAST search against the whole genome sequence of the genome. On the top of the section, you can find a link to the used query feature. It leads to the [[SEED_Viewer_Manual/Annotation|Annotation Page]]. You can select a different query feature using the drop down box and click the button '''Take this gene for tblastn search'''. <br />
<br />
The graphic shows the result of the tblastn search. It shows all found hit reagions. The hit is marked with a '''Q''' in the graphic. The region displays all features in the hit regions, colored by the frame each feature is in (See legend on top of the graphic). Dark colors mark that the features belong to the context subsystem. This way, you can see if the hit clusters with other features of the subsystem. If the hit ('''Q''') overlaps with an existing feature in the same frame, this feature might be the candidate you look for.<br />
<br />
[[Image:SearchGene2.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/CompareMetabolicReconstructionSEED Viewer Manual/CompareMetabolicReconstruction2008-12-02T11:26:14Z<p>DanielaBartels: /* Compare Metabolic Reconstruction */</p>
<hr />
<div>== Compare Metabolic Reconstruction ==<br />
<br />
This comparison is done on basis of the functions of all features of two genomes. The reference genome is called '''Organism A''', the comparison genome '''Organism B'''.<br />
<br />
Entering the page, you have already defined an '''Organism A''', as you followed a link e.g. from an [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the '''Organism A'''. Now you have to choose your '''Organism B''' using the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] on the page. Click '''select''' to start the computation.<br />
<br />
The resulting page will start with a header line showing the two genomes to compare. Behind the header, you find a button '''select other''' if you don't like the comparison genome. It will open an [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] to choose another comparison organism.<br />
<br />
[[Image:CompareMetaResult.png]]<br />
<br />
The first column of the [[WebComponents/Table|table]] ('''Presence''') tells you for each function, if it is present in ''A'', ''B'', or ''A and B''. The next three columns ('''Category''', '''Subcategory''' and '''Subsystem''') describe the subsystem the functional role belongs to. The functional role itself is displayed in column 5 ('''Role'''). <br />
<br />
The feature(s) that implement(s) the functional role in '''Organism A''' will appear in the next column. They are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. The following column '''SS active A''' tells you if the subsystem listed in the line is active in the Organism A, meaning that it has a valid variant code. The same information is shown for '''Organism B''' in the next two columns.<br />
<br />
If a role is not present for one of the organisms, a '''Find''' button will be displayed instead of the feature id. It leads to the [[SEED_Viewer_Manual/SearchGene|Search Gene Page]]. Here, you can search for a candidate for the function.<br />
<br />
If a feature is assigned with more than one functional role (multi-functional), it will appear once for each function in the table.<br />
<br />
You can export the contents of the table in ''tab-separated format'' using the '''save to file''' button.<br />
<br />
[[Image:CompareMetaReconst.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/BLASTDotPlotSEED Viewer Manual/BLASTDotPlot2008-12-02T09:45:25Z<p>DanielaBartels: /* BLAST Dot Plot */</p>
<hr />
<div>== BLAST Dot Plot ==<br />
<br />
This page shows a bidirectional comparison of two genomes. The data computed for the comparison is a protein-based BLAST of the features of the two genomes. The dot plot displays all bidirectional protein hits between the two genomes. In the example, the two genomes are very close, which results in a diagonal line.<br />
<br />
If you are interested in a certain region of the plot, you can select a window in the plot using the left mouse button. The coordinates of the region are then put in the text fields above the graphics. You can view this region in the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for a genome using the button '''display region'''. The region will be pre-selected in the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]].<br />
<br />
[[Image:BLASTDotPlot1.png]]<br />
<br />
[[Image:BLASTDotPlot2.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/MultiGenomeCompareSEED Viewer Manual/MultiGenomeCompare2008-12-01T12:10:33Z<p>DanielaBartels: /* Result */</p>
<hr />
<div>== Multi Genome Compare ==<br />
<br />
This page provides a way to compare a chosen organism against on or many others on the basis of the feature sequences (protein).<br />
<br />
=== Start the computation ===<br />
<br />
To start a Multi Genome Comparison, you have to fulfill three steps:<br />
<br />
1) '''Select Reference Genome'''<br />
<br />
The reference genome is used as a basis for the comparison. All selected genomes (step 2) will be projected on this one. Click [[SEED_Viewer_Manual/OrganismSelect|here]] to see how to select an organism.<br />
<br />
2) '''Select Comparison Organisms'''<br />
<br />
You can select maximal four organisms to project on the reference genome. <br />
<br />
3) '''Compute'''<br />
<br />
Press '''compute''' to start the computation. This may take while, as the system computes a bidirectional BLAST comparison of each genome to the reference genome. <br />
<br />
=== Result ===<br />
<br />
At the top of the result page you will see a list of the genomes involved in the comparison again. After each comparison genome, there is a button '''BlastDotPlot''' that leads to a [[SEED_Viewer_Manual/BLASTDotPlot|dot plot of the BLAST comparison]] between the comparison organism and the reference genome. <br />
<br />
You can use the link '''change organism selection''' on top of the table if the selection does not fit. <br />
<br />
[[Image:MCGResulta.png]]<br />
<br />
The colored [[WebComponents/Table|table]] below shows the outcome of the bidirectional BLAST comparisons between each comparison genome and the reference genome, projected on the reference genome. The colors in the table depicts the '''Percent protein sequence identity''' of each gene to it's ortholog in the reference genome. The legend on top of the table describes the coloring.<br />
<br />
[[Image:MCGResultb.png]]<br />
<br />
The first three columns of the table refer to the chosen reference genome ('''Contig''', '''Gene''' and '''Length'''). The Gene ID links to the <br />
[[SEED_Viewer_Manual/Annotation|Annotation]] page for the feature. <br />
<br />
The best BLAST hit of the query feature in the comparison genome is shown in three columns in the table ('''Hit''', '''Contig''' and '''Gene'''). The color of the hit is determined by the percent identity of the query and the hit. No color means there is no hit. The '''Hit''' column contains a '-' (no hit), 'uni' or 'bi'. The '''bi''' stands for ''bidirectional best hit'', meaning that the reverse hit from the comparison genome to the reference genome is also the best hit (That's not always true if a genome contains many close paralogs for a feature). If it's not a bidirectional hit, it shows '''uni''' for uni-directional. Each feature ID is again linked to the feature's [[SEED_Viewer_Manual/Annotation|Annotation Page]]. Hovering over a cell in the table will show a tooltip with some information about the feature.<br />
<br />
The contents of the table can be exported in ''tab-separated format'' using the '''export''' button on top of the table. The filters below the buttons refer to the percent identity for the features of each genome. You can choose to filter the table for the percent identity above or below a certain value for each genome, and also in combination. Use the button '''clear all filters''' to reset the table.<br />
<br />
[[Image:MCGResultc.png]]<br />
<br />
The circular image right to the table is a whole genome view for the reference genome. Each circle represents a projection of a comparison genome to the reference genome, in the same order as in the table. Keep in mind that the table as well as the graphic only shows features of the comparison genomes, that are hit by the reference genome. The order of the features is determined by the reference genome.<br />
<br />
If you click on a line in the graphics, the table will update and show the area that was clicked in the graphic. The red circle in the graphic determines the area the table currently displays.<br />
<br />
<br />
[[Image:MCGResult2.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/ShowSeqsSEED Viewer Manual/ShowSeqs2008-12-01T11:34:42Z<p>DanielaBartels: /* Display fasta sequences */</p>
<hr />
<div>== Display fasta sequences ==<br />
<br />
This page shows sequences of given features. Usually, you enter this page from a page where you have selected a number of sequences. You can download or display the sequences using the '''Download Sequences''' or '''Show Fasta''' buttons. <br />
<br />
The header of the fasta sequences is in the format ''>feature_id [Organism id] [annotation]''. <br />
<br />
You can choose between three options for the sequences:<br />
<br />
1) '''DNA Sequence'''<br />
<br />
Provides you with the DNA sequence in fasta format. <br />
<br />
2) '''DNA Sequence with flanking'''<br />
<br />
Also DNA sequence, but it adds a number of bases upstream and downstream to the feature. The sequence of the feature will then appear in upper-case letters, while the flanking sequences will be lower-case.<br />
<br />
3) '''Protein Sequence'''<br />
<br />
The protein sequence (translated DNA). <br />
<br />
[[Image:ShowSeqs.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/FunctionalRolesSEED Viewer Manual/FunctionalRoles2008-11-26T17:07:41Z<p>TobiasPaczian: /* Functional Role Page */</p>
<hr />
<div>== Functional Role Page ==<br />
<br />
This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [http://www.geneontology.org GeneOntology] classifications for a role. The link leads to the GO-Viewer [http://amigo.geneontology.org/cgi-bin/amigo/search.cgi AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number.<br />
<br />
The right part of the table gives an overview of the assignments of the functional role to SEED features. '''Number of Occurrences''' is the total number of features that are assigned with the role. '''Number of Organisms''' is the number of different organisms that contain at least one feature assigned with the role. Then they are devided by domains of the organisms (Archaea, Bacteria, Eukaryota or Virus). <br />
<br />
[[Image:FunctionalRole1.png]]<br />
<br />
The table below lists all features that are assigned with the functional role. The feature ID links to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for the feature. The organism link in the second column of the table points to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. The domain of the organism is depicted in the third column.<br />
<br />
You can download the table in ''comma-separated format'' using the '''export table''' button. To gain access the sequences of the listed features, press the '''show sequences''' button that opens the [[SEED_Viewer_Manual/ShowSeqs|Sequence]] page.<br />
<br />
[[Image:FunctionalRole2.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/DownloadOrganismSEED Viewer Manual/DownloadOrganism2008-11-26T16:23:15Z<p>DanielaBartels: /* Download Organism */</p>
<hr />
<div>== Download Organism ==<br />
<br />
This page offers you to download a variaty of different information and formats of data for an organism. If you want to access other information than accessible on this page you can go to out ftp site linked on the page. <br />
<br />
All features of the genome in protein FASTA format can be downloaded using the '''FASTA''' link. Right-click the link and save the content to a file to get a fasta file.<br />
<br />
To get a tab-separated table of all features and the information visible in the table below, click the '''Tabular''' link and save it to a file.<br />
<br />
If you only want to download features with certain characteristics, you can filter the [[WebComponents/Table|table]] on the page and click the '''export''' button. This will let you save a file with only the filtered features.<br />
<br />
[[Image:ExportOrganism.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/RegisterSEED Viewer Manual/Register2008-11-26T15:50:19Z<p>DanielaBartels: </p>
<hr />
<div>== Register ==<br />
<br />
Registering for a service (RAST, MetaRAST, or others) can be done using this registry form.<br />
<br />
Use the first tab of the [[WebComponents/Tabview|TabView]] to register if you have not already got an account for an other service. If you already have an account (for example, you have a user login for the RAST, but now you need access to the MetaRAST), use the second tab, where you only have to state your login and email to register for this service.<br />
<br />
Put in your personal information and click the button '''Request'''. An administrator will check your request and send you a user login or give you access to the requested service.<br />
<br />
[[Image:Register.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/UserManagementSEED Viewer Manual/UserManagement2008-11-26T14:52:30Z<p>DanielaBartels: /* User Management */</p>
<hr />
<div>== User Management ==<br />
<br />
The user management page offers options to change your user information (first name, last name, email and password). Click '''perform changes''' to save your changes. The password has to be typed in twice to avoid typing errors. <br />
<br />
The section '''Your Group Memberships''' lists user groups you are part of. A user group is build if a right should be added to a whole group of people, e.g. a group of people annotating a genome. Click on the link to view all members of a group. <br />
<br />
[[Image:UserManagement.png]]</div>DanielaBartels /wiki/WebComponents/LoginWebComponents/Login2008-11-26T14:12:30Z<p>DanielaBartels: /* Login Box */</p>
<hr />
<div>== Login Box ==<br />
<br />
If you have a User Login for SEED applications (SeedViewer, RAST, MetaRAST and others), you can easily log in using the Login Box present on the right side of the menu page on every page (unless you are already logged in).<br />
<br />
Enter your login in the first textbox, and your password in the second, then press return.<br />
<br />
[[Image:LoginBox.png]]<br />
<br />
After logging in, the Login Box will be replaced by your first and last name, together with the small items displayed below. The little door icon lets you log out. The other icon leads to your [[SEED_Viewer_Manual/UserManagement|User Management Page]].<br />
<br />
[[Image:LoginIcons.png]]<br />
<br />
If you don't have a login yet, but you wish to use applications or functions a login is required for (e.g. upload a genome to the [[RAST_Tutorial|RAST]]), use the link '''[[SEED_Viewer_Manual/Register|Register]]''' in the '''[[SEED_Viewer_Manual/Menu#Help Menu|Help Menu]]'''.</div>DanielaBartels /wiki/SEED_Viewer_Manual/FindSEED Viewer Manual/Find2008-11-26T11:38:05Z<p>DanielaBartels: /* What it does */</p>
<hr />
<div>== Find ==<br />
<br />
The Find Window is present on every page in the SeedViewer. Type in a text and press the button '''Find''' to search for your keyword.<br />
<br />
[[Image:FindWindow.png]]<br />
<br />
=== What it does ===<br />
<br />
The given keyword is used to first search different categories in the SEED database for a perfect match (fast search) in the following order:<br />
<br />
- Organisms<br />
<br />
- Subsystem Names<br />
<br />
- Feature IDs<br />
<br />
- Aliases to Features<br />
<br />
If a perfect match is found, it returns the page for that match in that category (e.g. if you search for Escherichia coli K12, the SeedViewer will load the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism.<br />
<br />
If '''no''' perfect match is found, it will search the following categories using an infix search (meaning that the keyword can be part of an organism, functional role etc.):<br />
<br />
- Functional Roles<br />
<br />
- Organisms<br />
<br />
- Subsystem Names<br />
<br />
- Feature Annotations<br />
<br />
The infix search may take a while. You will get a page that lists all search results for your search.<br />
<br />
=== Special features ===<br />
<br />
If your page has a defined genome (e.g. [[SEED_Viewer_Manual/OrganismPage|Organism Page]], [[SEED_Viewer_Manual/Annotation|Annotation Page]]), you can type in a number and it will open the Annotation page for the feature ending with that number. This is helpful if you want to browse through Annotation pages of many features in a genome.</div>DanielaBartels /wiki/WebComponentsWebComponents2008-11-26T11:07:08Z<p>DanielaBartels: </p>
<hr />
<div>== Web Components ==<br />
<br />
'''Web Components''' are widgets that were developed in context of the SEED applications, e.g. the [[SEED_Viewer_Manual|SeedViewer]], the [[RAST_Tutorial|RAST]] and others. The components provide functionality that is needed on many pages. Most prominent components are the '''[[WebComponents/Table|Table]]''' and the '''[[WebComponents/Tabview|TabView]]'''. <br />
<br />
See a list of common components on how to use them:<br />
<br />
[[WebComponents/ListSelect|List Select]]<br />
<br />
[[WebComponents/Login|LoginBox]]<br />
<br />
[[WebComponents/FilterSelect|Filter Select]]<br />
<br />
[[WebComponents/Table|Table]]<br />
<br />
[[WebComponents/Tabview|TabView]]</div>DanielaBartels /wiki/WebComponents/TableWebComponents/Table2008-11-26T09:15:48Z<p>TobiasPaczian: /* Export */</p>
<hr />
<div>== Table ==<br />
<br />
The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. Most of these functions of the table are implemented by JavaScript functions. That means, it does not lead to a reload of the page. The page ''knows'' all the information, but only part of it is displayed. The display is then manipulated using JavaScript functions. <br />
<br />
A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below.<br />
<br />
The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey.<br />
<br />
[[Image:Table1.png]]<br />
<br />
=== Browsing ===<br />
<br />
The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. Just press return after changing the number to change the display of your table. <br />
<br />
To browse through the table you can click the links '''<<first''', '''<<prev''', '''next>>''' and '''last>>'''. The links only appear if there is e.g. a next page. The text in the middle of the links will tell you which items are currently displayed.<br />
<br />
[[Image:TableBrowse.png]]<br />
<br />
=== Sorting ===<br />
<br />
You can sort the contents of the table by each column using the little arrows next to the column header. The sorting is done using JavaScript, meaning that it does not reload the page. <br />
<br />
[[Image:TableSort.png]]<br />
<br />
=== Filtering ===<br />
<br />
Different kinds of filters can be applied to the table data. The table always uses all filters for all columns at once. This means that if you may want to check if other filters are active, if the result of filtering a column is not what you expect. Often, a '''clear all filters''' button is made available on top of the page.<br />
<br />
One filter is simply a text field that does an infix search (meaning that if the word you type in the text field is part of a word in the cells of a cell in the respective column, the row will be visible).<br />
<br />
[[Image:TableFilter1.png]]<br />
<br />
The combo box filter is usually used if only a small number of different values are used in a column. These values appear in the combo box if you click the arrow next to the textfield. Choose one and the table will filter automatically.<br />
<br />
[[Image:TableFilter2.png]]<br />
<br />
If a column consists of numbers, you will often get a filter using operators ('''>''', '''<''', '''=''' and others). You can choose one of these operators, and put a number into the text field below the operator to filter the table.<br />
<br />
[[Image:TableFilter3.png]]<br />
<br />
=== Export ===<br />
<br />
For most tables, you will find an '''export''' button on the page. This will let you download the data of the table in '''.tsv''' format. This tab-separated text can be opened with many editors and spreadsheet tools (i.e. Microsoft Excel).</div>DanielaBartels /wiki/WebComponents/TabviewWebComponents/Tabview2008-11-26T08:58:41Z<p>TobiasPaczian: /* The TabView */</p>
<hr />
<div>== The TabView ==<br />
<br />
The TabView component is used on many pages in the [[SEED_Viewer_Manual|SeedViewer]]. It is useful at places where you have different options to access data or you need to fulfill a task step-by-step.<br />
<br />
The entire content of the TabView is loaded when you enter the page. Clicking a different tab only displays the data which was hidden before.<br />
At the top of the TabView, you can access the different tabs. In the example (SeedViewer Mainpage), the chosen tab is white, while all hidden tabs have a green header. Click on the green header to activate the respective tab.<br />
<br />
[[Image:TabView.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/SubsystemsSEED Viewer Manual/Subsystems2008-11-25T14:23:40Z<p>DanielaBartels: /* Scenarios */</p>
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<div>== Subsystems ==<br />
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A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system. <br />
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The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes. The last tab displays the [[Glossary#Scenarios|Scenarios]] for the subsystem.<br />
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=== Diagram ===<br />
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The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.<br />
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The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green. <br />
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[[Image:SubsystemDiagram.png]]<br />
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=== Functional Roles ===<br />
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This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function. <br />
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The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet. <br />
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The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.<br />
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The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.<br />
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GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.<br />
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The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.<br />
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[[Image:SubsystemFRs.png]]<br />
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=== Spreadsheet ===<br />
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The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem. <br />
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The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name. <br />
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The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.<br />
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For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary#Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''. <br />
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The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism.<br />
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'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes. <br />
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The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants.<br />
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All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.<br />
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The control table above the spreadsheet table lets you change the display in the table:<br />
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Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column. <br />
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The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.<br />
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[[Image:SubsystemSpreadsheet.png]]<br />
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=== Description ===<br />
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The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.<br />
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=== Additional Notes ===<br />
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As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.<br />
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=== Scenarios ===<br />
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The table shows all scenarios that occur in the subsystem. You can see the scenario name, the '''Input Compounds''', the '''Output Compounds''' and a checkbox to decide if you want to see the scenario painted on the [http://www.genome.jp/kegg/ KEGG] map below. If you change the selection of scenarios to paint on the map, click the button '''Paint Map(s)''' to reload the map.<br />
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You can also select an organism to highlight on the map. Therefore, click the '''Select Organism''' button to get an [[SEED_Viewer_Manual/OrganismSelect|Organism Select]]. After choosing an organism, click the button '''Highlight Reactions for Organism''' to mark the enzymes present in the organism with black boxes.<br />
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[[Image:SubsystemScenTabs.png]]<br />
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The [http://www.genome.jp/kegg/ KEGG] map is the first tab of a [[WebComponents/Tabview|TabView]]. The header of the tab includes a link to the map at [http://www.genome.jp/kegg/ KEGG]. Each enzyme in the map is painted with all colors of the scenarios it is part of. A color legend is presented on the right side of the map.<br />
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The second tab of the [[WebComponents/Tabview|TabView]] shows all reactions that are not shown on the map, but are part of the subsystem. <br />
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[[Image:SubsystemScenarios.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/EvidenceSEED Viewer Manual/Evidence2008-11-24T15:23:59Z<p>DanielaBartels: /* Similarities */</p>
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<div>The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''.<br />
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If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]].<br />
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== Visual Protein Evidence ==<br />
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After loading the Evidence Page, the first tab of the [[WebComponents/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.<br />
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=== Location ===<br />
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'''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein.<br />
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[[Image:EvidenceLocation.png]]<br />
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=== Domains ===<br />
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This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein).<br />
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Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.<br />
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[[Image:EvidenceDomain.png]]<br />
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=== Similarities ===<br />
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This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color.<br />
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Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature.<br />
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The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.<br />
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If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.<br />
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[[Image:EvidenceSims1.png]]<br />
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[[Image:EvidenceHoverSim.png]]<br />
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To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view.<br />
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[[Image:EvidenceFil1.png]]<br />
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== Tabular Protein Evidence ==<br />
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Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab.<br />
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=== Similarities ===<br />
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The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.<br />
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The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]].<br />
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The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''.<br />
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The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence'''). <br />
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The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color.<br />
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'''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell.<br />
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There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].<br />
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The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table.<br />
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[[Image:EvidenceSims2.png]]<br />
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You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a [[WebComponents/ListSelect|List Select]] with a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.<br />
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[[Image:EvidenceFilter.png]]<br />
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=== Domains ===<br />
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This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein).<br />
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The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain.<br />
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The table can be exported using the '''export table''' button.<br />
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Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.<br />
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[[Image:EvidenceDomTable.png]]<br />
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=== Identical Proteins ===<br />
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'''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity. <br />
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The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias.<br />
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[[Image:EvidenceEIPs.png]]<br />
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=== Functionally Coupled ===<br />
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This [[WebComponents/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature. <br />
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[[Image:EvidenceFCs.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/HomologClustersSEED Viewer Manual/HomologClusters2008-11-24T14:20:36Z<p>DanielaBartels: /* Homolog cluster */</p>
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<div>== Homolog cluster ==<br />
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This page shows the homolog cluster table for a given feature, where ''homology'' is inferred by similarity score. The ''cluster'' is computed using [[Glossary#Functional coupling|Functional coupling]] as a basis. For a given organism, only features which are in clusters are considered, and only a single feature (the one with the best similarity score) is reported. The table consists of maximal 50 homolog features, and the evalue cutoff is e -10.<br />
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On the top of the page a small table shows some information about the query feature. The '''Input Feature ID''' links to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for the feature. The '''Organism''' link leads to the respective [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The '''Cluster Size''' depicts how many features in that organism belong to the computed cluster. The '''Function''' of the query peg is depicted next, as well as '''Other functions in the cluster''', meaning the functions of the other features in that genome that are computed to belong to the cluster.<br />
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The following table of all features in the computed homolog cluster shows you the same information for each feature, as well as '''Aliases''' for that features in other databases. The column '''Cluster Functions''' includes the functions of the stated feature, which is marked in red.<br />
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[[Image:HomologClusters.png]]</div>DanielaBartels /wiki/SEED_Viewer_Manual/AnnotationSEED Viewer Manual/Annotation2008-11-21T11:45:24Z<p>TobiasPaczian: /* Compare Regions */</p>
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<div>== Annotation ==<br />
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The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes. <br />
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If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]].<br />
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=== The Annotation Overview ===<br />
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The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively.<br />
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The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry.<br />
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As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on.<br />
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The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature. <br />
The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome.<br />
'''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link.<br />
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Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group.<br />
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At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''.<br />
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'''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]].<br />
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'''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others.<br />
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To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''.<br />
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[[Image:AnnotationFeat.png]]<br />
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=== Reasons for Current Assignment ===<br />
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For information about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. In addition to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role.<br />
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[[Image:AnnotationAnnot.png]]<br />
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=== Compare Regions ===<br />
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The first line of the '''Compare Regions''' is a graphical display of the chromosomal neighborhood of the feature in its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. Feature overlaps are resolved by drawing the overlapping feature in a new line.<br />
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The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them. <br />
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'''Display Options''' are divided into two ''Regular'' and ''Advanced''. <br />
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In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. If you are logged in, the numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]].<br />
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[[Image:AnnotationComp.png]]<br />
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If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View. <br />
The '''Pinned CDS Selection''' refers to the chosen feature and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes. <br />
A '''PCH''' stands for [[Glossary#Pair_of_Close_Homologs_.28PCH.29|pair of close homologs]].<br />
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In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option.<br />
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The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected feature may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the feature.<br />
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The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs must have to the selected CDS in order for its region to be displayed.<br />
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Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''.<br />
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We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring.<br />
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[[Image:AnnotationAdv.png]]<br />
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The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. In addition to Start, Stop, Strand and Functional Role of the feature, you can see the columns ''FC'', ''SS'', ''Set'' and ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column lead to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature.<br />
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[[Image:AnnotationTabl.png]]</div>DanielaBartels