Re: Another Reverse Complement Question...

[Cristoforo]

I don't work with BioPerl, but they do have a reverse complement method, revcom and it can be used like this example:

#!/usr/bin/perl
use strict;
use warnings;
use 5.014;
use Bio::PrimarySeq;

my $seqobj = Bio::PrimarySeq->new(-seq      => 'ACTGTGGCGTCAACTG',
                                  -alphabet => 'dna',
                                  -id       => 'test');

say $seqobj->seq;
say $seqobj->revcom->seq;

__END__
*** print out

ACTGTGGCGTCAACTG
CAGTTGACGCCACAGT

But this doesn't do the translation you want: A => T, C => G, G => C and T => A. So, I don't know if this is any help.

Update: After examining the reversed complement sequence, I see indeed it performs the complement as you stated but it also reverses the sequence with the first letter in the original being complemented and last in the reversed sequence, the second in the original complemented and being next to last in the reversed complement sequence, etc.