[Bioperl-l] Seq::IO/clustalw

Liam Elbourne liam at mmb.usyd.edu.au
Sun Mar 28 21:58:33 EST 2004

Hi All,

Is there a quick way of substituting protein ids for accession codes. 
I've just done an clustalw alignment using DNA, and decided to use the  
protein sequences instead (not a very good alignment.......). Rather 
than substitute the protein ids manually, I wondered whether at the:

my $seqobj = $db->get_Stream_by_id(['x?????','af?????', etc, etc, etc);

step I could get the corresponding amino acid translation for the 
accession?. The sequences then get written to a file which is passed to 

     my $seq_out = Bio::SeqIO->new( -format => 'fasta',
                                  -file => "> $outfile");

     while( $aseq = $seqobj->next_seq() )

Liam Elbourne.

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