Technical Overview, dblist gpmnum

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This script searches the GPMDB for the proteins identified in a specific result file and displays them in groups of 20.

The one required argument is gpmnum, a GPMDB result file identifier of the form "GPMxxxNNNNNNNN", where "xxx" is one of the three-digit identifiers of the search machines that form a part of the GPM, and the "NNNNNNNN" is a sequentially assigned number unique within the "xxx" machine. Two optional arguments are proex and ltype. If proex is not supplied, it defaults to -1, and is used solely in forming the links that lead to protein-level information for identifications in this file. If the ltype argument is not supplied, it defaults to 2; this value is both passed on through links to protein-level information pages, but also controls the display of the label elements; choices that can be made are "ensembl", "ipi", "symbol" (the default), "ncbi" and "swiss".

Display Elements

  • a list of links to result file level information.
  • navigation links for the pages of results. The "best" link is a link back to
  • a dropdown menu to change the label display type.
  • the per-protein lines of information.

The links to result file level information are:

The per-protein pieces of information are:

  • the protein order number.
  • the expect value of this protein identification.
  • the accession number, according to the chosen label type.
  • a coverage diagram for this protein identification. This is an Adobe SVG element depicting the sections of the protein which are covered by the peptides identified for this protein in the data file.
  • an AJAX-generated identification comparison, comparing the quality of this identification to all other identifications of it.

This script uses the following tables: result, protein, peptide, proseq, paths.

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