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Not sure if this is much better than your code:

#! perl -slw use strict; my %invert; @invert{ qw[ A C G T ] } = qw[ T G C A ]; my $in = do{ local $/; <DATA> }; chomp $in; print $in; for my $p1 ( 1 .. length( $in ) -2 ) { next unless substr( $in, $p1, 1 ) eq $invert{ substr $in, $p1+1, 1 + }; my $pals = 0; for my $p2 ( 1 .. $p1 -1 ) { last unless substr( $in, $p1-$p2, 1 ) eq $invert{ substr $in, +$p1+$p2+1, 1 }; ++$pals; } if( $pals ) { printf "%s%s at %d\n", ' 'x($p1-$pals), substr( $in, $p1-$pals, ($pals+1)*2 ), $p1-$pals; } } __DATA__ AGAGGTCAGTCTGCATCGTATCGATCGTCGACGATCGATACGATGCAGACTGACGAGAG

Produces:

[13:44:54.28] C:\test>1085446 AGAGGTCAGTCTGCATCGTATCGATCGTCGACGATCGATACGATGCAGACTGACGAGAG TGCA at 11 ATCGAT at 19 CGATCG at 21 GTCAGTCTGCATCGTATCGATCGTCGACGATCGATACGATGCAGACTGAC at 4 CGATCG at 31 ATCGAT at 33 TGCA at 43

Modify to taste :)


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In reply to Re: Finding biological palindromes by BrowserUk
in thread Finding biological palindromes by TJCooper

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