[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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