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

Iddo Friedberg idoerg at burnham.org
Thu Dec 11 18:57:46 EST 2003

jordan swanson wrote:
> I've downloaded and installed blast and some FASTA
> databases for a lab I'm working for.  I have a user
> who is blasting (using blastx) against a list of
> clones.  Unfortunately, the database files I
> downloaded do not contain enough information for
> her(because they are fasta format)

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.

> This leads me to believe that I need a local copy of
> the genBank files.  I've downloaded gbpln[1-9].seq
> from NCBI. (we only need plant files).  Is it possible
> to blast against these gb files?  Also, what options
> do I need to use on formatdb to create the correct
> index files?

You can only formatdb from ASN.1 or Fasta formats.

> If my questions are out of place here, let me know and
> I'll desist.
> -Jordan M 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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