Hi everyone,

I'm pretty new to Perl, I'm trying to write a code for enzymatic digestion and have a problem with the regex in it; something like this:

So this would be for trypsine, it cuts after K or R, but only if there is no P after them.

#!/usr/bin/env perl
use warnings;

@proteins=qw(DAAAAATTLTTTAMTTTTTTCKMMFRPPPPPGGGGGGGGGGGG ALTAMCMNVWEIT
+YHKGSDVNRRASFAQPPPQPPPPLLAIKPASDASD);

for $protein (@proteins) {
    if ($protein =~ m/(KR)!P/g) {                       
                $protein =~ s/(KR)/$1=/;
                @new_peptides = split ('=',$protein);
    }
}

for (@new_peptides) {
    print "The peptide is $new_peptides\n";
}

[download]
I am getting no errors or warnings, but there is no output whatsoever, I'm guessing it has to do with the loop? Need some enlightening please. Many thanks in advance

Thanks all! Working now, and I also added more enzymes, selectable by getopts. Peptides printing alright, however, how could I track which peptide comes from which protein in order to make the printing a little more organised? I.e: Protein 1 Peptide 1 Protein 1 Peptide 2 ... Protein n Pepptide x

In reply to Bioinformatics: Regex loop, no output by TamaDP

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