Technical Overview, dblist label

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This script searches GPMDB for protein identifications based on accession number.

The one required arugment is label, which is a protein accession number. The results of the search are all identifications of the accession number supplied, ranked by increasing expect value and displayed twenty results at a time. Each row consists of the expect value, links to other data views and a coverage diagram. Optionally, the proex argument may be supplied; omitting it results in a default proex value of -1. This value is not used in the search, but is used to build the links to other scripts which expect it.

Display Elements

  • The count of identifications of this protein.
  • The information toolbar, a series of links to both internal and external pages of other information regarding this protein.
  • The human-readable information about this accession number, such as its given name (e.g., "Calumenin Precursor (Crocalbin)"), displayed with a yellow background.

The result navigation links are found directly above the currently displayed results; "best" is a link back to, "previous X" and "next X", where X is a number between 1 and 20 depending on your location within the result set, and "Last", which will display the 20 results with the highest expect scores.

Above the table of results is a tag cloud made up of the top twenty most common terms found in the project notes associated with each result file.

The per-identification links are:

  • G, a link to, to view all proteins in the model containing this specific identification of the protein in question.
  • P, a link to, to view full information regarding this specific protein identification.
  • O, a link to, to view gene ontology information associated with the set of proteins in the original data file.

The coverage diagram is an Adobe SVG element depicting the sections of the protein which are covered by the peptides identified for this protein in the original data file. The column header for this area is a toggle control which will switch between the display of the coverage diagram and any user-supplied project notes associated with the result file.

This script uses the following tables: protein, result, proseq, enspmapdb.gpmnotes.

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