Green white peptide algorithm

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This algorithm is used to generate diagrams in GPM display pages that indicate the peptides which are unlikely to be observed in a proteomics experiment. A "green" peptide is unlikely to be observed and all other peptides are "white".
This algorithm is used to generate diagrams in GPM display pages that indicate the peptides which are unlikely to be observed in a proteomics experiment. A "green" peptide is unlikely to be observed and all other peptides are "white".
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==Algorithm==
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==Green/White Peptide Algorithm==
For each peptide sequence, if any of the following rules are met, the peptide is rated "green":
For each peptide sequence, if any of the following rules are met, the peptide is rated "green":

Latest revision as of 14:37, 6 November 2012

This algorithm is used to generate diagrams in GPM display pages that indicate the peptides which are unlikely to be observed in a proteomics experiment. A "green" peptide is unlikely to be observed and all other peptides are "white".

Green/White Peptide Algorithm

For each peptide sequence, if any of the following rules are met, the peptide is rated "green":

  1. the peptide has < 6 residues;
  2. the peptide has > 35 residues;
  3. the peptide has a domain with 7 or more residues in a row exclusively from the list "LIVMACFWY"; or
  4. if the peptide has > 10 residues and > 67% of its residues from the list "LIVMFWY".

All other peptides are "white".

The Perl code that performs this assessment in GPM is the subroutine "unlikely", found in "/thegpm-cgi/common.pl".

Retrieved from "http://wiki.thegpm.org/wiki/Green_white_peptide_algorithm"
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