[Biojava-dev] Biojava Interface to BLAST web/remote services

[Andreas Prlic]

although using a different API this system is similar to the sequence
search service provided by Pfam ...
http://pfam.sanger.ac.uk/help#services
Andreas

On Thu, Jun 4, 2009 at 12:38 PM, Scooter Willis <HWillis at scripps.edu> wrote:
> Looks like the rolled their own URL interface and did not do a WSDL. Not a
> big deal but does appear they have some sort of submit get a "ticket" and
> then check back with the "ticket" identifier for the results. The BioJava
> API would hide the transport layer so you could use a custom URL approach or
> web services.
>
> Not sure how the other WSDL interfaces handle long running tasks but I
> assume the Web Services can handle a call that takes say 5 minutes to
> respond without timing out. Some process would need to distinguish between a
> long running server task and a server that is no longer responding.
>
> Scooter
> ________________________________
> From: biojava-dev-bounces at lists.open-bio.org on behalf of Andreas Prlic
> Sent: Thu 6/4/2009 5:12 AM
> To: Sylvain Foisy
> Cc: biojava-dev at lists.open-bio.org
> Subject: Re: [Biojava-dev] Biojava Interface to BLAST web/remote services
>
> Hi Sylvain,
>
> Do you mean the URL api for the NCBI Blast searches? Could not find a
> link for a WSDL...
> http://www.ncbi.nlm.nih.gov/BLAST/developer.shtml
>
> Andreas
>
>
> On Tue, Jun 2, 2009 at 6:26 PM, Sylvain Foisy
> <sylvain.foisy at diploide.net> wrote:
>> Hi,
>>
>> In response to Scooter and from using some of these BLAST implementations
>> in
>> the past, I would suggest that we use the QBlast service from NCI first
>> for
>> a number of reasons:
>>
>> - It has been in operation for a long time and its usage is well
>> documented;
>>
>> - Because of this, there is few chances that it will change;
>>
>> - Coming from NCBI, it will probably be there for some time to come ;-)
>>
>> Our friends at BioPerl have been using this technique for a long time now
>> with the BioPerl Module:Bio::Tools::Run::RemoteBlast module. We might try
>> to
>> emulate at first and of course, do better :-)
>>
>> Any inputs?
>>
>> Best regards
>>
>> Sylvain
>>
>> ===================================================================
>>
>>  Sylvain Foisy, Ph. D.
>>  Consultant Bio-informatique / Bioinformatics
>>  Diploide.net - TI pour la vie / IT for Life
>>
>>  Courriel: sylvain.foisy at diploide.net
>>  Web: http://www.diploide.net
>>
>> ===================================================================
>>
>>
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