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alignment software

Nick Morris Nick.Morris at Dartmouth.Edu
Thu Apr 10 05:34:52 EST 1997

In article <5iic0h$39s$1 at vishnu.jussieu.fr>, Michel SEIGNEURET
<michel at biophy.jussieu.fr> wrote:

> Dear Collegues.
> My question is probably trivial but I am a newcomer to this field and
> I could not find a FAQ on this.
> I currently often do BLAST or FASTA searches of particular protein sequences 
> against the SWISSPROT or PIR databases though the WWW. The problem is that the
> internet connection of my lab is slow. I am thus thinking of doing such
> searches locally after downloading the complete database. Could somebody
> suggest me a freely available software that allows one to do a BLAST or FASTA 
> alignment search locally ? 
> Thank you in advance.
> Michel Seigneuret
> Lab. de Biophysique Cellulaire et RMN
> Universite Paris 7
> France

If your internet connection is so slow that you can't do BLAST by WWW then
dowloading the database (if possible?) may take days!

My suggestion would be to do the BLAST searches by e-mail, the results
would then be returned by e-mail.  It may not be quite as user friendly as
the WWW but at least you won't have to sit at the computer waiting for
things to happen. Also, the e-mail can be formatted so that an HTML
document is returned so you can still make use of the direct links to the
protein/DNA entry in the database.

I hope this helps,


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