[BiO BB] QBLAST

yhuang4 at memphis.edu yhuang4 at memphis.edu
Mon Dec 1 11:26:32 EST 2003


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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