Thanks for all your ideas. It was really useful . Parveen Date: Wed, 30 Nov 2005 09:42:51 -0800 (PST) From: "W. Eric Trull" <[EMAIL PROTECTED]> Subject: [Biojava-l] help on blast To: biojava-l@biojava.org Cc: [EMAIL PROTECTED], [EMAIL PROTECTED] Message-ID: < [EMAIL PROTECTED]> 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 _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
