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14 non-PAUSE users.

Christopher Fields
and 1 contributors


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 bandwith
  # 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: http://www.ebi.ac.uk/cgi-bin/dbfetch.

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 Bio::DB::WebDBSeqI.

This module retrieves entries from EBI although it retrives 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>


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