[Biojava-l] BLAST/Java interface

[Patrick McConnell]

---------------------- Forwarded by Patrick McConnell/CanCtr/mc/Duke on
08/23/2002 09:19 AM ---------------------------

From:  Patrick McConnell on 08/23/2002 08:57 AM

To:    nathan whitehouse <nlwhitehouse@yahoo.com>
cc:

Subject:    Re: [Biojava-l] BLAST/Java interface  (Document link: Patrick
       McConnell)

I have developed a blast web service that takes all of the standard blast
parameters and returns NCBI blast XML.  I have also generated classes that
correspond to the blast XML complex types, so you don't even have to know
anything about XML.

The web service is developed to be hosted by GLUE, but it should not be a
problem to port it to another web service container.

I have release the source, as well as the compiled Java code.  I include
the jar for the web services container, so you do not need to download
anything else to get up and running.

See: http://mendel.mc.duke.edu:1755/services/blast/ for full source code
and compiled classes.

I am currently developing servlets/jsps as a web front-end to this, which
will format the XML into an NCBI-like html page.  Thus, it will be a full
package for serving blast.

Good luck,

-Patrick




nathan whitehouse <nlwhitehouse@yahoo.com>@biojava.org on 08/22/2002
04:39:05 PM

Sent by:    biojava-l-admin@biojava.org


To:    biojava-l@biojava.org
cc:

Subject:    [Biojava-l] BLAST/Java interface


Hello people at BioJava,

  I'm modifying an existing Java applet-servlet used
by this lab.

  People want us to add BLAST to this applet.

  Anybody know of a good way to do this?

   Are there convenient BLAST libraries to call from
the servlet?  We've talked about calling a C or C++
library using the JNI.  I've looked around and it
seems that there's no modularized BLAST lying around
that would make this easy.
  The simple way to do it is just call BLASTAll from
the shell with its arguments.  But this is a hack; I
want to know if there is a better way to pass objects
in and out of BLAST.

  Thanks!
  Nathan

  Nathan Whitehouse
  Shaulsky Lab
  Baylor College of Medicine
  Houston, Texas, USA

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