Technical Overview, protein.pl

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The required arguments are ''path'', ''proex'', ''label'', ''homolog'', ''uid'', ''npep'' and ''ltype''.  ''path'' is the file system path to the GPM result file.  ''proex'', ''uid'', ''homolog'' and ''npep'' are used to create links to other scripts on GPMDB.  ''ltype'' controls the appearance of display elements on the page.
The required arguments are ''path'', ''proex'', ''label'', ''homolog'', ''uid'', ''npep'' and ''ltype''.  ''path'' is the file system path to the GPM result file.  ''proex'', ''uid'', ''homolog'' and ''npep'' are used to create links to other scripts on GPMDB.  ''ltype'' controls the appearance of display elements on the page.
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Liz, I have known this for years. Glad people are fialnly realizing the power of their emotions. As a long time sufferer of IBS I have had to learn to control my emotions because if I get really upset my IBS really acts up. On another note, stress really does a number on me as well. Stress can kill folks and people don't realize what a power affect stress can have on their lives. It can manifest differently in people but I find I grind my teeth and my husband chews his nails. For some folks it can even mean losing their hair or rashes. Yoga and meditation are the best medicines for keeping your emotions in check.
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== Display Elements ==
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*a table of links to both GPM and external resources.
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*a form to control the display of both the [[Technical Overview, AJAX content|AJAX-generated]] content and list of peptides used to identify this protein.
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*a [[Technical Overview, Coverage diagram|coverage diagram]] of the peptides identified for this protein.
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*(validate): a link to [[Technical Overview, dblist_v.pl|dblist_v.pl]].
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*(mrm): a link to [[Technical Overview, peak_search.pl|peak_search.pl]], if this protein is contained in the [[Technical Overview#peakdb|peakdb]] tables.
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*a colour-coded display of the residues in this protein sequence. Red residues are part of a peptide in the GPM file; green residues are areas of the protein unlikely to be covered by peptides due to either their length or hydrophobicity.
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*a table of peptide identifications for this protein:
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**'''spectrum''': the identifier for the spectrum associated with this peptide.
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**'''log(e)''': the base-10 logarithm of the chances that the identification of this peptide is a random match.  E.g., a log(e) score of -3.0 corresponds to a  1 in 1000 chance of a false positive identification.
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**'''log(I)''': the base-10 logarithm of the raw intensities associated with this spectrum.
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**'''m+h''': the weight of this peptide, in Daltons.
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**'''delta''': the difference between the measured mass and theoretical mass of this peptide.
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**'''z''': the charge of the peptide, as measured by the instrument used to generate the data file given to the search software on the GPM.
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**'''sequence''': the residue sequence of the peptide.  Residues highlighted in blue are modified proteins. Residues highlighted in red are mutations.
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**'''n''' or '''ω''': [[Technical Overview, AJAX content|AJAX-generated]] content about this peptide. '''n''' corresponds to the count of identifications of this peptide in the GPMDB.  '''ω''' corresponds to the relative frequency of identification of this peptide for this protein in this GPM result file.
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*'''Protein Information''': information about this protein from external sources (e.g., ENSEMBL or IPI), cached on the GPM.

Revision as of 13:57, 28 September 2012

This script displays information about a single protein identification from a GPM result file.

The required arguments are path, proex, label, homolog, uid, npep and ltype. path is the file system path to the GPM result file. proex, uid, homolog and npep are used to create links to other scripts on GPMDB. ltype controls the appearance of display elements on the page.

Display Elements

  • a table of links to both GPM and external resources.
  • a form to control the display of both the AJAX-generated content and list of peptides used to identify this protein.
  • a coverage diagram of the peptides identified for this protein.
  • (validate): a link to dblist_v.pl.
  • (mrm): a link to peak_search.pl, if this protein is contained in the peakdb tables.
  • a colour-coded display of the residues in this protein sequence. Red residues are part of a peptide in the GPM file; green residues are areas of the protein unlikely to be covered by peptides due to either their length or hydrophobicity.
  • a table of peptide identifications for this protein:
    • spectrum: the identifier for the spectrum associated with this peptide.
    • log(e): the base-10 logarithm of the chances that the identification of this peptide is a random match. E.g., a log(e) score of -3.0 corresponds to a 1 in 1000 chance of a false positive identification.
    • log(I): the base-10 logarithm of the raw intensities associated with this spectrum.
    • m+h: the weight of this peptide, in Daltons.
    • delta: the difference between the measured mass and theoretical mass of this peptide.
    • z: the charge of the peptide, as measured by the instrument used to generate the data file given to the search software on the GPM.
    • sequence: the residue sequence of the peptide. Residues highlighted in blue are modified proteins. Residues highlighted in red are mutations.
    • n or ω: AJAX-generated content about this peptide. n corresponds to the count of identifications of this peptide in the GPMDB. ω corresponds to the relative frequency of identification of this peptide for this protein in this GPM result file.
  • Protein Information: information about this protein from external sources (e.g., ENSEMBL or IPI), cached on the GPM.
Retrieved from "http://wiki.thegpm.org/wiki/Technical_Overview,_protein.pl"
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