Technical Overview

Revision as of 18:11, 17 February 2009

This page will serve as an index to the explanation pages for the entities that make up the GPM.

Database Updates

• Technical Overview, GPMDB Updates: the steps taken to add new information to GPMDB.

Database Tables

• Technical Overview, table relationships: how the tables of GPMDB work together.
• Technical Overview, result table: the table of GPM result files.
• Technical Overview, protein table: the table of identified proteins.
• Technical Overview, peptide table: the table of identified peptides.
• Technical Overview, aa table: the table of amino acid modifications and mutations.
• Technical Overview, best_expect table: the table of the lowest (best) expect score and identification count for each protein.
• Technical Overview, peptide_word_index table: the table that drives tag searches of peptide sequences.
• Technical Overview, paths table: the table of GPM file archive locations.
• Technical Overview, peptide_mut table: the table of peptides with known point mutations.
• Technical Overview, project table: the project table.
• Technical Overview, proseq table: the table of protein sequences dictated by RNA.

Software

• Technical Overview, dblist_label.pl: to search by accession number, and display the twenty best results.
• Technical Overview, dblist_label_all.pl: to search by accession number, and display all results by pages.
• Technical Overview, dblist_gpmnum.pl: to search by GPM result file number.
• Technical Overview, dblist_pep.pl: to search by residue sequence.
• Technical Overview, dblist_keyword.pl: to search protein descriptions by keyword.
• Technical Overview, plist.pl: to view a summary of the protein identifications in a GPM result file.
• Technical Overview, protein.pl: to view all identifications of a protein.
• Technical Overview, pgo.pl: to view the gene ontology of the proteins in a GPM result file.
• Technical Overview, dblist_protein_mut.pl: to view peptides with known SNAPs.

Display Elements

• Technical Overview, Coverage diagram: a graphical depiction of peptide coverage for both a specific protein identification and total peptide coverage for all identifications of a specific protein.
• Technical Overview, AJAX content: asynchronously retrieved pieces of metadata about peptides and proteins.