BLAST sequence comparisons

[Bill Pearson]

Christopher Coward (Path) <cc122 at mole.bio.cam.ac.uk> wrote:
>Does anyone know if there is a server that will compare two (or more?) 
>sequences with each other using the BLAST algorithm? Ie I don't want to 
>do a database search, just see if there are regions of homolgy between 
>two sequence. 

You can use lalign, which is part of the fasta package, to do this.
Just set the gap and extension penalties very very (infinitely, e.g.
-10000) high.  This will give you the same thing you would get with
blastp.

The fasta package is available from uvaarpa.virginia.edu in pub/fasta.
fasta20x.shar(.Z) has the code you need to set gap penalties easily.
You can also use prss to check statistical significance.

Bill Pearson
-- 
wrp at virginia.EDU
Dept. of Biochemistry #440
U. of Virginia
Charlottesville, VA 22908