[BiO BB] Is it possible to Blast against genBank files

Iddo Friedberg idoerg at burnham.org
Thu Dec 18 16:00:25 EST 2003

Biopython has something that can do that. Maybe Bioperl too. Let me know 
if you want the Python code.


jordan swanson wrote:
>>You mean that the BLAST results only have the Fasta
>>file annotation in 
>>them. Well, AFAIK, the only input to formatdb is
>>Fasta or ASN.1. The 
>>output, anyhow, would be a one-liner.
>>How about giving her the output in HTML (-T option)?
>>blast automatically 
>>builds a link from each hit to the NCBI page. So
>>using a browser, your 
>>coworker can skim the one-line annotation, and then
>>click & delve into 
>>the more interesting ones.
> We did try that, however with the large number of
> sequences she needed to look up, she was black-listed
> from their machine.  We need to find the full GenBank
> entry given a particular identifier, unfortunately the
> easiest way I've found so far seems to be the Entrez
> system, and that appears to not be possible to
> download.  Is there another way to get the full
> genbank entry given the identifier?
> ---
> Jordan Swanson
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Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171

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