retrieving sequences after a BLAST?

Arne Mueller a.mueller at icrf.icnet.uk
Tue Jun 8 09:15:06 EST 1999

"Dr. Greg Quinn" wrote:
> If you are doing a netBlast with GCG, I believe that NetFetch can parse
> the blast output file and fetch the cited sequences from the NIH site.
> Also, Nigel Brown's program, MVIEW will 'extract' alignments from a
> BLAST search to create a multiple alignment (with some caveats); this
> sometimes obviates the need to pull sequences depending on what you
> have in mind for the database matches.


Mview aligns the sequences reported in the blastfile which is very often
only a fragment of the sequence (the highest scoring part) but mview is
able to produce output in html and link the sequences to SRS so you can
click on the sequence names and get the full database entry from SRS.
Have a look at http://mathbio.nimr.mrc.ac.uk/nbrown/mview/


Arne Mueller
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44 Lincoln's Inn Fields
London WC2A 3PX, U.K.
phone : +44-(0)171 2693405      | Fax : +44-(0)171 269 3258
email : a.mueller at icrf.icnet.uk | http://www.icnet.uk/bmm/

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