[Bioperl-l] Parsing clustalw alignments

Ryan Golhar golharam at umdnj.edu
Sun Jan 29 12:48:34 EST 2006

I can't figure this out from the documentation.  In fact, I'm not sure
its possible:

I have a bunch of clustalw alignments in GCG (MSF) format.  Each
alignment consists of three sequences.  I want to get the sequences
including the gaps from the alignment.  

I'm trying to use Bio::AlignIO to read the alignment file, then trying
to get each sequence from the alignment. I tried doing this:

$seqio = Bio::AlignIO->new(-format => 'clustalw', -file =>
my $aln = $seqio->next_aln();
$seq1 = $aln->next_seq()->seq;

Getting the sequence from the alignment isn't working and I'm not sure
how to do it.  Does anyone have any ideas as to what I might try?

Ryan Golhar  -  golharam at umdnj.edu
The Informatics Institute of UMDNJ

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