[Biojava-l] Blast

[David Waring]

I have set up a system that calls a local version of blastall. With it you
can blast a SequenceDB against your local blast database and get back a list
of SequenceSimilarityResults. This also provides access to the sequences in
the blast database via a call to fastacmd. So you have access to the query
and subject sequences from the SequenceSimliaritySearchResult. As Thomas
mentions there must be enviroment specific information available for this to
work. This is why I have not tried to put it into biojava. I also have
similar classes for cross_match and RepeatMasker.

I have my own way of handling the enviroment variables which is a bit
specific to our environment where we have both NTs and Unix boxes all
looking at the same drives via Samba mounts with a single biojava
installation for both Unix and NT. Environment specific info (paths to
executables, tmp directories, etc.) is stored in flat files, one for Unix
and one for Windows. I have an Object I call Constants (a historical name we
could change it to something more meaningful) which reads the flat files and
provides static access to the various enviroment info. It uses the
java.Properties class for this. So the flat file is in the format.
	variablename=value
	anothervariable=anothervalue
	# and we have comments
This makes maintainence pretty simple.

So we could have a single file that would have to exist in the ClassPath
that the Constants object would look for.

Of course there are probably better ways to do this. And perhaps someone
would have ideas about how to abstract it a bit so we could handle cross
network activity as well as local system calls. If we can come up with a
design, I would be happy to move my things over to biojava.


> -----Original Message-----

>
> On Tue, Nov 06, 2001 at 04:02:53AM -0800, SAMEER MOHTA wrote:
> > Hi All,
> >
> > Can we fire a Blast search using BioJava (without
> > using Blast client). If so then what all packaes are
> > used for the same and what is the procedure.
> > I suppose this facility is available in BioPerl. But i
> > want to know is there any way in BioJava.
>
> BioJava has a good solid parser for blast output, but not
> currently any way of launching the blast program itself.  I
> think the expectation is that you would do that yourself
> using Java process objects, or possibly talk across the network
> to some kind of blast server.
>
> I can see the advantages of having some kind of blast-launching
> shortcut system.  The trouble with this is that there are lots of
> variables: path to executable, which version you're using, which
> options to support, etc., etc.
>
> We should look at what Bioperl do for this.
>
> > other thing, is there any facility in BioJava to parse
> > OMIM data.
>
> Not yet.  Would be nice to have, though :-)
>
>    Thomas.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l