fasta-blast replies, thanks

Frederic PLEWNIAK plewniak at titus.u-strasbg.fr
Mon Sep 4 07:02:00 EST 2000


On 1 Sep 2000 10:58:07 +0100, "Neil Saunders"
<neil.saunders at unsw.edu.au> wrote:

>Good idea.  This was my problem:  I wanted to extract the top hits from a
>BLAST search and obtain the sequences as a FASTA file, so as to do a
>multiple alignment including my query sequence.  These were the suggestions.
>
May I add a 7th suggestion if your problem was to extract top
sequences from a BlastP search and do a multiple alignment with them
and your query?

You may want to submit your query sequence (in FastA format ;o) ) to
the DbClustal Web server:

	http://igbmc.u-strasbg.fr:8080/DbClustal/dbclustal.html

This server is quite recent (a week or so) and still requires some
work but you may use it already.

The server will then:

 1) Blast search the latest Swissprot+SPtrEMBL database with your
    sequence
 2) Extract anchors between your query and the Blast top hits with
    Ballast
 3) Do a multiple alignment with top hits and your query, you'll get 	
    the results as an MSF file

This method was recently published by Thompson J.D. et al. in Nucleic
Acid Research (Vol.28, pp 2919-2926).

If you want to get more info about Ballast and the anchors you may
have a look at http://igbmc.u-strasbg.fr:8080/ballast.html (the paper
is in press) or get in touch with me.

All the best,

Fred










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