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

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...
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Re^3: How do I find match patterns between two DNA sequences?
by BrowserUk (Patriarch) on Oct 26, 2010 at 15:56 UTC 

    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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