Technical Overview, dblist pep

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This searches the GPM for instances of specific peptide sequences, and displays some summary information about them.

The one required argument is peptides, which is a delimited set of peptide sequences. Before querying, any duplicate sequences will be removed.

Three optional arguments are sort, format and filter_labels. sort is the sort order of the # Obs column, which defaults to descending order, placing the peptide with the highest number of identifications at the top. format controls if the output of the list should be HTML for viewing online, or 'excel', for opening in a spreadsheet program.

Display Elements

  • text boxes for submitting search parameters:
    • Peptides: takes a delimited list of peptide sequences on which to search.
    • Accession Filter: one or more protein accession numbers in this box will cause the labels to act as a filter; any peptides that were identified as part of one of the proteins listed in the box will be displayed separately from those that were not.
  • the search results:
    • #: the result number.
    • Peptide: the peptide sequence, formatted with a space every twenty residues. The peptide is a link to for that peptide.
    • # Obs: the number of times this peptide has been identified in GPMDB.
    • Labels: a list of proteins in which this peptide has been observed. The accession numbers are links to for that protein accession number.

This script uses the following tables: in GPMDB, peptide_index, proseq, protein, peptide.

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