BLAST sequence comparisons
wrp at reed0.med.Virginia.EDU
Mon Mar 13 14:30:18 EST 1995
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
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
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.
wrp at virginia.EDU
Dept. of Biochemistry #440
U. of Virginia
Charlottesville, VA 22908
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