Yes and thanks! I made a slight adjustment. The true reason for generating these substrings is to see if there are any palindromes and I need to check all possible substrings of the fasta string (here 800 chars). This code is not checking for palindromes (but is trivial to add that). I just needed to get the munging part correct. (Just to run the program as is created an 86 MB file, which I won't be doing - just printing out the palindromes instead). But, it does take some time and with a larger fasta string, may take a while to just test every substring.

Thanks everyone. I'll be working at this for a while now. The reason I am doing this is because I saw that Mathmatica does a palindrome check in pretty terse terms (someone had a link to Mathmatica here in the Monks a few days ago).

Chris 

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

my $str = do {local $/; <DATA>};
$str =~ s/\s+//g;
my $len = length $str;

do {
    printf "%3d : %s\n", $_, substr( $str, $_, $len )
        for 0 .. ( length( $str ) - $len );
} while (--$len > 3);

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In reply to Re^2: Capture Lookahead by Cristoforo
in thread Capture Lookahead by Anonymous Monk

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