Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::DB::RefSeq - Database object interface for RefSeq retrieval


         use Bio::DB::RefSeq;

         $db = Bio::DB::RefSeq->new();

         # most of the time RefSeq_ID eq RefSeq acc
         $seq = $db->get_Seq_by_id('NM_006732'); # RefSeq ID
         print "accession is ", $seq->accession_number, "\n";

         # or changeing to accession number and Fasta format ...
         $seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq ACC
         print "seq is ", $seq->seq, "\n";

         # especially when using versions, you better be prepared
         # in not getting what what want
         eval {
             $seq = $db->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION
         print "accesion is ", $seq->accession_number, "\n" unless $@;

         # or ... best when downloading very large files, prevents
         # keeping all of the file in memory

         # also don't want features, just sequence so let's save bandwidth
         # and request Fasta sequence
         $db = Bio::DB::RefSeq->new(-retrievaltype => 'tempfile' ,
                                      -format => 'fasta');
         my $seqio = $db->get_Stream_by_id(['NM_006732', 'NM_005252'] );
         while( my $seq  =  $seqio->next_seq ) {
               print "seqid is ", $seq->id, "\n";


       Allows the dynamic retrieval of sequence objects Bio::Seq from the RefSeq database using
       the dbfetch script at EBI:

       In order to make changes transparent we have host type (currently only ebi) and location
       (defaults to ebi) separated out.  This allows later additions of more servers in different
       geographical locations.

       The functionality of this module is inherited from Bio::DB::DBFetch which implements

       This module retrieves entries from EBI although it retrieves database entries produced at
       NCBI. When read into bioperl objects, the parser for GenBank format it used. RefSeq is a
       NONSTANDARD GenBank file so be ready for surprises.


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AUTHOR - Heikki Lehvaslaiho

       Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _