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Introduction:

"Perl and it's Application to Proteomics"

If you have the mass spec. protein database searching tool SEQUEST provided by Thermo Finnigan Corporation then you already have Perl installed on your PC, that means that you can start playing today.  Don't know what Perl is, then find out with an introductory article at "The Perl Journal".  Starting to get interested, find out "How Perl Saved the Human Genome Project" with an article by Lincoln Stein at the BioPerl Project.  If you want to get Perl go to the CPAN  or Active State sites, then you can write and run scripts to do almost anything you want.  The O'Riley series of books on Perl are about the best books on the subject.  For additional references take a look at;  Learning Perl, by Schwartz and Christiansen Programming Perl, by Wall, Schwartz and Christiansen Perl Cookbook, by Christiansen and Torkington.

To learn more about the power of the Perl programming language check out the links below. 

Table of Contents (click the heading to jump to the section or just scroll down)

  The Perl Journal
  Perl.Com
  Lincoln Stein
  The BioPerl Project
  BITS (Bio Informatics Technology & Systems)
  Active State
  Roberts Perl Tutorial
  City of Hope

	The Perl Journal "TPJ is the only magazine devoted to Perl, featuring in-depth articles from Perl experts. TPJ online offers full text articles dedicated to the perl script development community, source code from every issue, and an extensive back issue archive."
	Perl.Com "The Source for Perl"   CPAN - Comprehensive Perl Archive Network modules, scripts, ports, source code etc... "Regular expressions are to strings what math is to numbers" quote found at the perl journal site  FASTA libraries are ALL strings.
	Lincoln Stein's Home Page at Cold Spring Harbor Laboratory- This is a great site.   Genome Informatics, a class at CSH taught by Steve Rozen and Lincoln Stein.  This class is high recommended.  Lincoln Stein's "How Perl Saved the Human Genome Project" from the Perl Journal.
	The Bioperl Project "is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research."  Get on the bioperl mailing email list here. -
	Active State, "Programming for the people" Get your own free win32 copy of Perl. -
	City of Hope, "Programs for screening peptide MS/MS before Sequest searching and for establishing screening parameters (9 KB.zip file)"  down load from City of Hope. -

Method for Screening Peptide Fragment Ion Mass Spectra Prior to Database Searching -Full Article (PDF,210 K) Roger E. Moore, Mary K. Young, and Terry D. Lee