alignment software

James McInerney J.McInerney at
Thu Apr 10 08:17:26 EST 1997

Michel SEIGNEURET 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.

You can get FastA from:

you are going to need a beefy computer for big searches, but I like the
package and it does quite a lot of cool things.


James O. McInerney               email: J.mcinerney at
Senior Scientific Officer,       phone: +44 171 938 9247
Department of Zoology,           Fax:   +44 171 938 9158
The Natural History Museum,
Cromwell Road,                    
London SW7 5BD.                  

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