Technical Overview

From TheGPMWiki

Revision as of 19:58, 17 February 2009 by WikiSysop (Talk | contribs)

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.

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.

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, and display the twenty most reliably identified proteins from it.
Technical Overview, dblist_gpmnum_all.pl: to search by GPM result file number, and display all proteins identified from it by pages.
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, pgel.pl: to view a simulated two-dimensional gel of the proteins in a GPM result file.
Technical Overview, phplctab.pl: to view calculated HPLC information about the peptides in a GPM result file.
Technical Overview, ptissue.pl: to view proteins in a GPM result file in terms of BTO relationships.
Technical Overview, ppath.pl: to view proteins in a GPM result file in their KEGG pathways.
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.

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.
Technical Overview, protein information toolbar: a collection of internal and external links to further information regarding a protein accession number.