Will this help?

use strict;

my %sequences;

while (<DATA>) {
  chomp;
  $sequences{$_} = $.;
}

for my $seq (keys %sequences) {
  my $rev_compl = get_rev_compl($seq);
  print "$seq matches $rev_compl on line $sequences{$rev_compl}\n"
    if exists $sequences{$rev_compl};
}

sub get_rev_compl {
  my ($seq) = @_;
  $seq =~ tr/GCAT/CGTA/;
  return reverse $seq;
}
1;
__DATA__
GATTACA
TTAGCAA
CATCATC
TTGCTAA
TGTAATC
GATGATG

[download]

I put the sequences into a hash instead of an array to (hopefully) increase the lookup speed. This won't work if the sequences aren't unique, though.

Hanlon's Razor - "Never attribute to malice that which can be adequately explained by stupidity"

In reply to Re: string complement question by Art_XIV
in thread string complement question by Anonymous Monk

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