[Bioperl-l] blast program to run locally on windows

[Raghunath Verabelli]

Thanks Chris.

I have installed everything, but unable to get the
blast hits from the database file. I get this message:

BLASTP 2.2.13 [Nov-27-2005]


Reference: Altschul, Stephen F., Thomas L. Madden,
Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of
protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= target48
         (115 letters)

Database: temp 
           2,093,771 sequences; 757,160,754 total
letters



 ***** No hits found ******

  Database: temp
    Posted date:  Nov 11, 2005  3:50 PM
  Number of letters in database: 757,160,754
  Number of sequences in database:  2,093,771




I also see following error messages:

[NULL_Caption] WARNING:  [000.000]  target48: Unable
to open BLOSUM62
[NULL_Caption] WARNING:  [000.000]  target48:
BlastScoreBlkMatFill returned non-zero status
[NULL_Caption] WARNING:  [000.000]  target48:
SetUpBlastSearch failed.


Any ideas how to resolve this issue?

thanks,
Raghu


--- Chris Fields <cjfields at uiuc.edu> wrote:

> Use the NCBI win32 binaries and either download your
> database from NCBI or
> build your own custom databases using formatdb:
> 
> http://www.ncbi.nih.gov/BLAST/download.shtml
> 
> More up-to-date help is available here:
> 
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/
> 
>
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/pc_setup.html
> 
> Instructions on how to format your own databases is
> here:
> 
>
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatdb_fastacmd.html
> 
> Chris
> 
> > -----Original Message-----
> > From: Raghunath Verabelli
> [mailto:iamvela at yahoo.com]
> > Sent: Tuesday, April 25, 2006 11:08 AM
> > To: Chris Fields; 'Jason Stajich'
> > Cc: bioperl-l at lists.open-bio.org
> > Subject: blast program to run locally on windows
> > 
> > Hi All,
> > 
> > I am looking for a blast program ('blastp') that I
> can
> > run locally on windows platform instead of using
> > NCBI's blast over web.
> > 
> > Do you know any such programs?
> > 
> > I checked Washington University's blast program,
> but
> > looks like they do not support it on windows
> platform:
> > http://blast.wustl.edu/blast/README.html#platforms
> > 
> > 
> > Any other alternatives?
> > 
> > Please let me know if you are aware of any
> 'blastp'
> > program equivalent to WU blast for Windows.
> > 
> > Thanks in advance,
> > Raghu
> > 
> > 
> > 
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam
> protection around
> > http://mail.yahoo.com
> 
> 


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com