Technical Overview, dblist protein mut.pl

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Revision as of 22:54, 18 February 2009

This searches GPMDB for instances of peptides from a specific protein that contain a known SNAP. This differs from the action of dblist_pep_modmass.pl which searches for modifications, not mutations.

The required argument label is a protein accession number for the protein in which you wish to locate mutations. The optional arguments are proex, offset and display. The proex argument is used in link creation to other pages in the GPM. The offset argument controls the first result to view, and defaults to zero to show the first result. The display argument is used to create links to dblist_pep_modmass.pl.

Display Elements

• the human-readable detains regarding the protein accession number, offset with a highlighted background.
• navigation links to page through the results of the search, twenty results per page.
• the search results:
  • #: the result number.
  • log(e): the expect value. This is the base-10 logarithm of the chances of this peptide identification was an accidental, random assignment. E.g., if the expect value is -4.0, the odds of this identification being erroneous is 1 in 10,000.
  • m+h: the mass of the peptide, in Daltons.
  • delta: the difference between the mass as measured by the instrument that generated the data file that was submitted to the GPM's search software and the theoretically calculated mass of the peptide based on the residue sequence.
  • z: the charge of the peptide, as measured by the instrument that generated the data file that was submitted to the GPM's search software.
  • Mut pos: a compound field.
    • The first element is the "standard" residue, followed by the residue's position in the protein, and suffixed with the residue that is the result of the mutation. E.g., "A[82]V" should be read as "alanine at protein residue position 82 mutated to valine."
    • The second element is the standard name for this SNAP.
  • peptide: a compound field.
    • The first element is the peptide sequence, bracketed by up to four residues of context from the full protein sequence.
    • The second element appears when there is more than one peptide identification for this protein with the same SNAP. If there is text that reads (X more), with X as a number, clicking this text will display the other peptides from this protein that have the same mutation at the same location.
    • The third element is a number in parentheses, e.g. "(85)", which denotes the number of identification of this peptide sequence across all peptides in GPMDB. This number is one piece of AJAX-generated content that appears on result, protein and peptide displays in the GPM.

This script uses the following tables: in EnspMapDB, map. In GPMDB, paths, result, protein, peptide, peptide_mut, proseq, aa.