[BiO BB] Java API for BLAST?

Joe Landman landman at scalableinformatics.com
Fri Dec 9 19:02:02 EST 2005

Hi Ahmed:

Ahmed Moustafa wrote:
> Hi Joe,
> I thought of switching my project to Perl because I found BioPerl had 
> more functionalities and more "documentation" than BioJava but am trying 
> first to stay with Java, otherwise will go to BioPerl.

My apologies about not being clearer.  I am not suggesting a port to 
Perl, just hooking in the previously developed modules through some sort 
of inter-language call.  In Perl it is fairly easy to do with the 
Inline::* modules, and I believe it is fairly easy with Python and Java. 
   Thats it... not advocating re-inventing your program in a new 
language, just using what might be available in another language that 
can help.


> Thanks!
> Ahmed
> On 12/9/2005 9:45 AM, Joe Landman wrote:
>> Hi Ahmed:
>>   You might look into hooking into the BioPerl bits from Java (RMI I 
>> think).  This shouldn't be too difficult.
>> Joe
>> Ahmed Moustafa wrote:
>>> Hi All!
>>> Is there some sort of a Java package to do BLAST search (remote or 
>>> local)? I went through BioJava and I could not find something like 
>>> that, it seemed there was only a parser for the BLAST XML output.
>>> Thanks in advance!
>>> Ahmed
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Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
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