(New page: This searches GPMDB for instances of peptides from a specific protein that contain given modification. This differs from the action of [[Technical Overview, dblist_protein_mod.pl|dblist_p...) |
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- | This searches GPMDB for instances of peptides from a specific protein that contain given modification. This differs from the action of [[Technical Overview, dblist_protein_mod.pl|dblist_protein_mod.pl]] which searches for proteins with known SNAPS, not mutations. | + | This searches GPMDB for instances of peptides from a specific protein that contain a given modification. This differs from the action of [[Technical Overview, dblist_protein_mod.pl|dblist_protein_mod.pl]] which searches for proteins with known SNAPS, not mutations. |
The two required arguments are ''label'' and ''modmass''. The ''label'' argument is a protein accession number for the protein in which you wish to locate modifications. The ''modmass'' argument is a mass modification (positive or negative), followed by an "at" symbol ('''@'''), followed by the residues on which the modification may be located. E.g, phosphorylation can be searched for with a ''modmass'' argument of "80@STY". | The two required arguments are ''label'' and ''modmass''. The ''label'' argument is a protein accession number for the protein in which you wish to locate modifications. The ''modmass'' argument is a mass modification (positive or negative), followed by an "at" symbol ('''@'''), followed by the residues on which the modification may be located. E.g, phosphorylation can be searched for with a ''modmass'' argument of "80@STY". |
This searches GPMDB for instances of peptides from a specific protein that contain a given modification. This differs from the action of dblist_protein_mod.pl which searches for proteins with known SNAPS, not mutations.
The two required arguments are label and modmass. The label argument is a protein accession number for the protein in which you wish to locate modifications. The modmass argument is a mass modification (positive or negative), followed by an "at" symbol (@), followed by the residues on which the modification may be located. E.g, phosphorylation can be searched for with a modmass argument of "80@STY".
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 control the appearance of the form at the top of the page; a value of 1 displays a form tailored to searching for phosphorylation, and a value of 0 displays a form where custom modifications may be entered.
This script uses the following tables: in EnspMapDB, map. In GPMDB, paths, result, protein, peptide, proseq, aa.