[Bioperl-l] acc does not exist

Brent and Johnetta Smith bdsjls at qx.net
Mon Jun 9 02:23:44 EDT 2003

I just recently installed BioPerl 1.2.1 on RedHat v9.0.  I'm trying to
execute the bptutorial script:

  use Bio::Perl;
  # this script will only work with an internet connection
  # on the computer it is run on
  $seq_object = get_sequence('genbank',"AF421111");
  write_sequence(">test.fasta", 'fasta', $seq_object) ;
and I receive the following error:

MSG: acc does not exist
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
STACK Bio::Perl::get_sequence
STACK toplevel bpTest.pl:10
I am absolutely 100% certain that the accession number exists on GenBank
(I verified and re-verified several times by going directly to their web
site).  Also, when "genbank" is changed to "swissprot" and a valid
accession number for swissprot is put in place of the AF421111 then it
works perfectly.  I have installed BioPerl on another RedHat 9.0
computer and it was working with both swissprot and genbank last time I
checked (last Tuesday).

Any suggestions?

Thank you.

Also, if this question is not appropriate for this list then please let
me know where to go for a users list.

Brent and Johnetta Smith <bdsjls at qx.net>

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