BLAST sequence comparisons

Bill Pearson wrp at
Mon Mar 13 14:30:18 EST 1995

Christopher Coward (Path) <cc122 at> 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

The fasta package is available from 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

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