[Biojava-l] BLAST/Java interface

[Wiepert, Mathieu]

Hi,

I haven't read through all the posts, but I thought this was a neat solution, a Web service.  Someday, I would hope that NCBI provides this.  But if you can host your own service, then this looks like an answer, code is there to look at...


http://mendel.mc.duke.edu:8090/services/blast/


-mat


> -----Original Message-----
> From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> Sent: Friday, August 23, 2002 8:18 AM
> To: biojava-l@biojava.org
> Subject: Re: [Biojava-l] BLAST/Java interface
> 
> 
> 
> ---------------------- 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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