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Bio::DB::RefSeq(3pm) User Contributed Perl Documentation Bio::DB::RefSeq(3pm)


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 nucleotide database using the dbfetch script at EBI:

At this time the module specifically retrieves nucleotide sequences only.

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 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.


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

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 _

2019-12-30 perl v5.30.0