retrieving sequences after a BLAST?

Francis Durst francis.durst at bota-ulp.u-strasbg.fr
Wed Jun 9 12:51:57 EST 1999


In article <375D256A.D78C6733 at icrf.icnet.uk> Arne Mueller <a.mueller at icrf.icnet.uk> writes:
>From: Arne Mueller <a.mueller at icrf.icnet.uk>
>Subject: Re: retrieving sequences after a BLAST?
>Date: Tue, 08 Jun 1999 15:15:06 +0100

>"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.

>Hi,

>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/

>        greetings,
>        Arne

>-- 
>Arne Mueller
>Biomolecular Modelling Laboratory

You may also use Octopus by Patrick Durand, which displays Blast (and Fasta) 
output, shows sequence info etc,  lets you select some or all sequences and 
displays them aligned in an editor window. You can save them as an .MSF file.

http://www.lmcp.jussieu.fr/~durand/HtmlDoc/software/octopus/octo_main.html

Francis

===============================================================
Francis Durst
CNRS / Institut de Biologie Moleculaire des Plantes
28, rue Goethe
67083 Strasbourg, France




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