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Retriving sequences from large local databases

Kevin Karplus karplus at cheep.cse.ucsc.edu
Wed Mar 16 06:59:21 EST 2005

In article <491dde49.0503080219.17666dac at posting.google.com>, Rolf wrote:
> I am running local blast on different databases. This works perfectly.
> The problem comes when I want to retrieve sequences from the large
> (and practically not possible to open) databases.
> Can this be done through the BioEdit program?
> Other programs?

If you are using NCBI blast, then the "fastacmd" program from NCBI can
retrieve your hits for you.  

fastacmd -d nr -i idfile > foo.fa

To get the ids, you might want to use the "-m 9" format for the output
of the blast query and -I T to turn on the full names. With this
format, you still have to extract the ids, but it is a simpler script
than with the usual nearly unparseable blast output.

Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors, ISCB)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
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