[Biojava-l] help on blast

[Parveen k]

Thanks for all your ideas. It was really useful .
Parveen

Date: Wed, 30 Nov 2005 09:42:51 -0800 (PST)
From: "W. Eric Trull" <wetrull at yahoo.com>
Subject: [Biojava-l] help on blast
To: biojava-l at biojava.org
Cc: fpepin at cs.mcgill.ca, k.parveen at gmail.com
Message-ID: < 20051130174251.95303.qmail at web81405.mail.mud.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

I have the same situation where I work, except I have a Swing client instead
of an applet.

I decided to use NCBI's BLAST implementation
(http://www.ncbi.nlm.nih.gov/BLAST/download.shtml) invoked using a command
to
org.biojava.utils.ExecRunner.  I then wrapped the whole thing in a Web
Service, which is easier and more flexible than using RMI IMHO.  NCBI's
BLAST
toolkit also contains the executable for building the BLAST database
from a FASTA sequence file (formatdb.exe).

Be sure to set the BLAST output option to XML (-m 7) and use a
org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade to parse the
output.  I had trouble using the default output as it is different under
Windows and *nix.  Look at the BioJava in Anger example of parsing BLAST
output if you need help here.

The one twist here is that you are constrained by the applet security model
which, I believe by default, will not allow you to go to a different server
for a Web Service unless you sign the applet.  Something for you to dig into
if you decided to use a Web Service.  The rest of my comments assume that
you
are going to go down the Web Service path.

For creation of the Web Service I'm using webMethods GLUE, but that requires
a $$ license.  I've used Apache's Axis/Tomcat to build web services before
and it is pretty easy to use.  Building a web service future proofs, IMO,
any
changes the powers that be may decided about the client side (i.e. "Now we
want a .NET application", etc.).

If you want a quick prototype, look at IBM's Web Services for Life Sciences
( http://www.alphaworks.ibm.com/tech/ws4LS).  They have a BLAST web service
that is downloadable and configurable to run in a local environment.
 However
their services are a bit dated (February 7, 2003).

One last thought.  I'm working under the constraint that I cannot send my
query sequence outside my local network.  If you DO NOT have this
restriction
and are just querying public databases, both the NCBI and PDB have web
services.  The PDB provides a SOAP over HTTP web service (WSDL at
http://pdbbeta.rcsb.org/pdbws/rcsbWebService?wsdl) which is currently BETA
but will go production January 1, 2006.  Point Axis at this WSDL to generate
client side code and then look for the blastQuery() methods.  The NCBI's web
service does not use SOAP, but provides an HTTP interface.  See
http://www.ncbi.nlm.nih.gov/BLAST/developer.shtml for documentation and a
Perl example.

Good luck!

-Eric Trull

--- Francois Pepin fpepin at cs.mcgill.ca wrote:

> Hi Parveen,
>
> This might not be as easy as you might like.
>
> The applet runs on the client, so you need the applet to communicate
> remotely to the server to send the sequence. Then the easiest way would
> be for the server to call blast on the command-line with the sequence
> (which is pretty easy), parse the result and send it back to the client
> applet.
>
> I think RMI could do this, but I've never had to play with it.
>
> Anyone has a better way to do this?
>
> Francois
>
> On Wed, 2005-11-30 at 16:04 +0530, Parveen k wrote:
> > Hi
> >    I'm pretty new to bioinformatics.i have to incorparate balst in my
> > applet.so that when the client enters the sequence ,it should perform
the
> > blast search against the database we have and return the result.can
> anyone
> > guide me in this regard.
> >
> > --
> > Regards
> > Parveen K
> >
> > YOU MAY SAY I AM A DREAMER, BUT  I AM NOT THE ONLY ONE.
> > I HOPE SOMEDAY YOU WILL JOIN US, AND THE WORLD WILL FOLLOW US.
> >                                   - JOHN LENNON
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
>
>
>
>


Thanks.

-W. Eric Trull


--
Regards
Parveen K
YOU MAY SAY I AM A DREAMER, BUT  I AM NOT THE ONLY ONE.
I HOPE SOMEDAY YOU WILL JOIN US, AND THE WORLD WILL FOLLOW US.
                                  - JOHN LENNON