Question: How do I get Genbank files by using wiki gene ids in bioperl?
gravatar for anp375
5.2 years ago by
anp375170 wrote:

My assignment is basically this:

  1. Take the first fifty gene_IDs from the chr1 and get GenBank reports via a remote blast. Remember the demo video from an earlier lecture?
  2. Return report with all input and output files. 

I'm using Bio::DB::Query::GenBank and Bio::DB::GenBank.

I'm basically sending in the IDs like this:

my $query = Bio::DB::Query::GenBank->new(-ids=>[195052,2981014,11127914]);

And then I make a DB::GenBank object and use the get_stream_by_query method on $query to get a list of sequences. The module description seems to say genbank can recognize wiki gene IDs but I'm getting this error:

MSG: Error from Genbank: Wrong UID 57576

Is there a way to convert it or will I have to do it through biomart?


I used biomart and tried out entrez and embl and they don't work either. What should I do?

genbank bioperl • 1.3k views
ADD COMMENTlink modified 3.7 years ago by Biostar ♦♦ 20 • written 5.2 years ago by anp375170
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1306 users visited in the last hour