BOL: Perl script to find palindromic regions in DNA sequences

BioScripts
Abhimanyu Singh
Perl script to find palindromic regions in DNA sequences

Perl script to find palindromic regions in DNA sequences

use strict;
use warnings;

my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix;
my $filename = $ARGV[0];
open(my $fh, '<:encoding(UTF-8)', $filename) or die "Could not open file '$filename' $!";

local $/ = '';

while (<$fh>) {
    chomp;
    my ($header, @lines) = split "\n";
    my $data = join '', @lines;

    print "$header\n$data\n";

    while ($data =~ /(?=($pp))/g) {
	my $end=($-[0]+length($1));
	my $n=(length($1)/2);
	my $len=length($1);
	my $midPoint = ($n == int $n) ? $n : int($n + 1);
	$midPoint=$midPoint+$-[0];
        print "$-[0]\t$midPoint\t$end\t$1\t$len\n" if length($1) > 100;
    }
}

__DATA__
>TRE|Q47404|Q47404 (409 AA) Glycosyl transferase [Escherichia coli]
MIFDASLKKLRKLFVNPIGFFRDSWFFNSKNKAEELLSPLKIKSKNIFIVAHLGQLKKAE
LFIQKFSRRSNFLIVLATKKNTEMPRLILEQMNKKLFSSYKLLFIPTEPNTFSLKKVIWF
YNVYKYIVLNSKAKDAYFMSYAQHYAIFIWLFKKNNIRCSLIEEGTGTYKTEKKKPLVNI
NFYSWIINSIILFHYPDLKFENVYGTFPNLLKEKFDAKKIFEFKTIPLVKSSTRMDNLIH

>seq1
TGAATTACTAGAAGTACTTAAAATGATGGTTGGAGGAAATATTCTTGATGATCAAATTGC
CGTTAAACTAGGATTTCTTATAAAGGAGGTTGGTAGTAAAATTCATGAAGATCATTAAGT

>TRE|Q8VRL9|Q8VRL9 (492 AA) SiaD [Neisseria meningitidis]
MLQKIRKALFHPKKFFQDSQWFATPLFSSFAPKSNLFIISTFAQLNQAHSLTKMQKLKNN
LLVILYTTQNMKMPKLIQKSVDKELFSVTYMFELPRKPGIVSPKKFLYIQRGYKKLLKTI
QPAHLYVMSFAGHYSSLLSLAKKMNITTHLVEEGTATYAPLLESFTYKPTKFEQRFVGNN
LHQKGYFDKFDILHVAFPEYAKKIFNANEYHRFFAHSGGISTSQSIAKIQDKYRISQNDY

BOL

Abhimanyu Singh

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Perl script to find palindromic regions in DNA sequences