Perl script to find palindromic regions in DNA sequences

Abhimanyu Singh — Tue, 12 Jun 2018 04:34:12 -0500

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: Perl script to find palindromic regions in DNA sequences

Perl script to find palindromic regions in DNA sequences