align 2 DNA sequences and find complementary regions

Question

I tried to find some clue in the list but I couldn't, so sorry if I ask a repeated topic

I am PERL beginner and I am trying to write a program in PERL that take two DNA sequences, calculate the reverse of the second one and find the maximum complementary regions between them, that is:

input:

CGTAAATCTATCTT
CATGCGTCTTTACG

output:

CGTAAATCTATCTT
GCATTT--------

I have no problem to find the reverse of the second sequence, however my programming skills in PERL are rudimentary. Do I need to use a combined for an foreach loops?

Answer 1

Perhaps this is what you want (crudely):

#!/usr/bin/env perl
use strict;
use warnings;
die unless @ARGV == 2 && length $ARGV[0] == length $ARGV[1];
my @seq1 = split //, $ARGV[0];
my @seq2 = split //, reverse $ARGV[1];
my @comp;
for my $n (0..@seq1-1) {
    if   ( ($seq1 [$n] eq 'A' && $seq2 [$n] eq 'T') 
        || ($seq1 [$n] eq 'T' && $seq2 [$n] eq 'A') 
        || ($seq1 [$n] eq 'G' && $seq2 [$n] eq 'C') 
        || ($seq1 [$n] eq 'C' && $seq2 [$n] eq 'G') ) {
        push @comp, $seq2[$n];
    }
    else {
        push @comp, '-';
    }
}
print @seq1, "\n", @comp, "\n";

...which when run:

# ./compseq CGTAAATCTATCTT CATGCGTCTTTACG
CGTAAATCTATCTT
GCATTT------A-