Friday, July 30, 2010

Bio::DB::Align::Rfam implemented

Bio::DB::Align::Rfam is implemented. However, a test using pfam alignment format failed. It seems there is something wrong with Bio::AlignIO::pfam. It needs to be solved later.

Now Bio::DB::Align::Rfam provides the sequence retrieval method by accession.

get_Aln_by_acc #retrieve the alignment using accession, and returns a Bio::SimpleAlign object

An example

my $dbobj=Bio::DB::Align->new(-db=>"rfam");
my $aln=$dbobj->get_Aln_by_acc("RF0001");
my $aln2=$dbobj->get_Aln_by_acc(-accession=>"RF0001",-alignment=>"full");

print $aln->length();

foreach my $seq ($aln->each_Seq) {
#do something

No comments:

Post a Comment