[Biojava-l] BLAST with Biojava

[Thomas Down]

Once upon a time, Ryan Golhar wrote:
> I'm looking through the documentation for biojava 1.3, and cannot find
> any reference to performing a BLAST search, or performing any type of
> SmithWaterman local alignment.  If its there, and I'm just not looking
> in the right place, can someone please direct me to where I can find
> information on this?  Thanks,

Launching external tools has never been a strong point for
BioJava, although if you're using the latest CVS version,
the ProcessTools class should provide some help.

However, having run blast/fasta/ssearch, there are tools which
will help you parse the output into useful objects.  For an
example, see:

    http://www.biojava.org/docs/bj_in_anger/BlastParser.htm

It's also possible to perform exhaustive alignment algorithms
(e.g. ssearch) entirely within BioJava using the dynamic programming
library.  If you've downloaded the source distribution, you could
take a look at the file demos/dp/PairwiseAlignment.java

Hope this helps,

    Thomas.