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

jordan swanson jordanmswanson at yahoo.com
Thu Dec 18 15:53:51 EST 2003

> 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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