[BiO BB] QBLAST

[yhuang4 at memphis.edu]

Dear Malcolm, 

my code submit batch queries to NCBI~{!/~}s server, check working process. 
If the result is available, download the result (JAVA code until 
here), then parse the result and output info according to the user 
(Bioperl for parsing). 

I understand my code is not useful for your purpose. Good luck for 
your project.

Yong


----- Original Message -----
From: "Cook, Malcolm" <MEC at Stowers-Institute.org>
Date: Monday, December 1, 2003 9:31 am
Subject: RE: [BiO BB] QBLAST

> Dear Yong Huang,
> 
> Thank you for taking the time to reply to my inquiry.
> 
> Do I understand correctly?  Have you written code which performs 
> blastsby talking to the NCBI's qBlast server?
> 
> If so, then your code is not helpful to me.  I am looking for an
> implementation of the Qblast server itself.  I am running programs 
> thatknow already how to talk to a QBlast server.  I want to point 
> thoseprograms to my own, in-house server.
> 
> If not, and you have implemented a blast server accordinag to the 
> Qblastprotocol, then I am still very interested and would like to 
> hear more.
> 
> Again, thanks for your time...
> 
> Regards,
> 
> Malcolm
> 
> 
> -----Original Message-----
> From: yhuang4 at memphis.edu [mailto:yhuang4 at memphis.edu] 
> Sent: Wednesday, November 26, 2003 8:48 AM
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] QBLAST
> 
> 
> Dear Malcolm,
> i just saw your post about QBLAST on Sep 2003. I wrote code for 
> batch 
> BLAST through QBLAST at begining of this year (my Master project 
> of 
> bioinformatics). The code was written in JAVA and Perl (Bioperl).
> 
> The flexibility of the code is:
> 0.good for single query or batch queries, BLASTn and BLASTp
> 1. observe the length of the first sequence of the batch queries, 
> and 
> automatically decide the parameters
> 2.dynamically check the working process
> 3.output format: HTML XML, Text
> 4.parse the result (Bioperl)and extraxt info by the user, e.g. top 
> 1, 
> or 2.. hit.
> 
> If you are still interested in QBLAST, please contact me.
> 
> 
> Yong Huang
> Feinstone center for genomic research
> University of Memphis
> (901) 678 2458
> Email: yhuang4 at memphis.edu
> 
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