Wednesday, July 14, 2010

First trial run for Bio::DB::Align::Pfam succeeded

I just got a trial run for some methods retrieving Pfam alignment sequences. It succeeded.

At the moment, this package (Bio::DB::Align::Pfam) aims at retrieving alignment sequences from Pfam using the accession number provided by the user. Calling the package can be:

my $obj = Bio::DB::Align::Pfam->new(); #or Bio::DB::Align->new(-database=>"Pfam") ???
my $aln = $obj->get_Aln_by_acc(-accession=>"PF00653",-alnType=>"seed",-format=>"fasta",-order=>"t",-case=>"l",-gap=>"default");

or simply as

my $aln = $obj->get_Aln_by_acc("PF00653");

The package will return a Bio::SimpleAlign object by simply one or two commands.

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