in reply to How do I find match patterns between two DNA sequences?

There is very good documentation about regexes in perlre, the regex you are looking for is really simple to construct, just remember that the first parentheses in a regex puts the matched contents into $1.

After that you just need to quotemeta the string and you can use that inside a regex

If you have further problems, just ask again, but post the code you have already written

  • Comment on Re: How do I find match patterns between two DNA sequences?

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Re^2: How do I find match patterns between two DNA sequences?
by Bio_student (Novice) on Oct 26, 2010 at 15:27 UTC
    What I mean is : If I have two sequences contain string sequences example : Seq1= AAGGTTCCTTAAGGAA and seq2= AAGGTTCCGGGGGGGGGG then how could I find the string which is similar at least 5 string in both sequences (i.e : AAGGTTCC or others) using Perl? I hope it's not make you confuse...
[reply]

      my $s1 = 'AAGGTTCCTTAAGGAA';;
my $s2 = 'AAGGTTCCGGGGGGGGGG';;

for my $start ( 0 .. length( $s1 ) - 5 ) { 
    for $len ( reverse 5 .. length( $s1 ) - $start ) { 
        my $n = substr $s1, $start, $len; 
        my $p2 = 1+index $s2, $n; 
        printf "s1:%d s2:%d '%s'\n", $start, $p2-1, $n if $p2;
    } 
};;
s1:0 s2:0 'AAGGTTCC'
s1:0 s2:0 'AAGGTTC'
s1:0 s2:0 'AAGGTT'
s1:0 s2:0 'AAGGT'
s1:1 s2:1 'AGGTTCC'
s1:1 s2:1 'AGGTTC'
s1:1 s2:1 'AGGTT'
s1:2 s2:2 'GGTTCC'
s1:2 s2:2 'GGTTC'
s1:3 s2:3 'GTTCC'

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