[Bioperl-l] revcom the multiple sequence alignment

[Jason Stajich]

I think this would work to update it in place though I haven't tried it myself

for my $seq ( $aln->each_seq ) {
 $seq->seq( $seq->revcom->seq );
}
$out->write_aln($aln);

This may also work - not entirely sure if there is any extra work done on the meta data (start/end) of the Seq object when this is done.  You may want to flip start/end for the sequences (the seqs are Bio::LocatableSeq objects) explicitly if not. Or you may not care about those data and can ignore.

   $seq = $seq->revcom

Jason
On Dec 6, 2011, at 8:09 AM, wenbin mei wrote:

> Hi,
> 
> I have a question about revcom the multiple sequence alignment. One way I
> can do convert the format into fasta and revcom individual sequences. I
> wonder is there a easy way to convert the multiple sequence alignment as a
> whole.  Thank you for help.
> 
> -best,
> wenbin
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