Difference between revisions of "SeedViewer Annotation"
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:This page offers access to the data relating to a feature. By default the Overview version of the page <br> | :This page offers access to the data relating to a feature. By default the Overview version of the page <br> | ||
:is initially displayed providing the feature's function assignment, source organism, the role it performs<br> | :is initially displayed providing the feature's function assignment, source organism, the role it performs<br> | ||
| − | :in a subsystem, and a graphic displaying it's genomic context. | + | :in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one<br> |
| + | :or more functional roles, each functional role's name will be displayed and linked to a [[SeedViewer_Functional_Role|SEED Viewer Functional Role page]]. | ||
| + | :A part of a feature's function that is not also a functional role is NOT linked. | ||
| + | |||
| + | :If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box <br> | ||
| + | :at the top of the page on the right. The functional role names and subsystem names are linked to the <br> | ||
| + | :[[SeedViewer_Functional_Role|SEED Viewer Functional Role page]] and the [[SeedViewer_Subsystem|SEED Viewer Subsystem page]]. | ||
:In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> | :In the graphic each line represents a different genome. The genome of the feature that is the subject of this page<br> | ||
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:a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> | :a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or <br> | ||
:number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> | :number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically<br> | ||
| − | :distant to the subject feature's genome. | + | :distant to the subject feature's genome. |
| + | :If there are no close genomes only a single line for the subject feature's genome will be present.<br> | ||
| + | :If no data for diverse genomes has been computed a message saying so will be be displayed.<br> | ||
Sequence Data | Sequence Data | ||
:From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> | :From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the<br> | ||
| − | this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. | + | :this feature's DNA sequence, DNA with flanking sequence or amino acid sequence. |
Tools | Tools | ||
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Literature | Literature | ||
| + | :This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source. | ||
Latest revision as of 14:24, 7 November 2006
SEED Viewer Annotation Page
Overview
- This page offers access to the data relating to a feature. By default the Overview version of the page
- is initially displayed providing the feature's function assignment, source organism, the role it performs
- in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one
- or more functional roles, each functional role's name will be displayed and linked to a SEED Viewer Functional Role page.
- A part of a feature's function that is not also a functional role is NOT linked.
- If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box
- at the top of the page on the right. The functional role names and subsystem names are linked to the
- SEED Viewer Functional Role page and the SEED Viewer Subsystem page.
- In the graphic each line represents a different genome. The genome of the feature that is the subject of this page
- is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have
- a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or
- number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically
- distant to the subject feature's genome.
- If there are no close genomes only a single line for the subject feature's genome will be present.
- If no data for diverse genomes has been computed a message saying so will be be displayed.
Sequence Data
- From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the
- this feature's DNA sequence, DNA with flanking sequence or amino acid sequence.
Tools
- From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools
- to analyze this feature:
- TMpred
- TMHMM
- Gram negative PSORT
- Gram negative SignalP
- Gram positive PSORT
- Gram positive SignalP
- LipoP
- InterProScan
- Radar
- PPSearch
- Gram negative CELLO
- Gram positive CELLO
- ProDom
Literature
- This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source.