Difference between revisions of "SEED Viewer Manual/Evidence"
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Revision as of 10:46, 24 November 2008
The Evidence Page is divided into two parts via a TabView: The Visual Protein Evidence and the Tabular Protein Evidence.
Visual Protein Evidence
Location
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 by 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.
Domains
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).
Additional tools can be accessed via the Feature Tools Menu in the menu bar.
Similarities
Tabular Protein Evidence
Similarities
Domains
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).
The 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.
The table can be exported using the export table button.
Additional tools can be accessed via the Feature Tools Menu in the menu bar.
Identical Proteins
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.
The first column of the 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.
Functionally Coupled
