[Biodevelopers] Is it source available for blastall

[Bala]

Hi Joe,
       Thanks for the information,
I found out the solution for that command
line parameter problem, the command I am 
trying to run is

#blastall -p blastp -d /usr/local/sge/db/pataa -i
/usr/local/sge/QUERY -M /usr/local/sge/db/BLOSUM62

the solotion is, instead of giving the matrix path
in the command line, set the enviroinment variable
"BLASTMAT".

  I didn't find .ncbirc file in my stand allown blast 
download from NCBI site, can you give me some info 
regrading .ncbirc file content and where to
put(location) of the file.

Thanks,
Bala.





--- Joe Landman <landman at scalableinformatics.com>
wrote:
> Hi Bala:
> 
>   Look on http://www.ncbi.nlm.nih.gov for the BLAST
> (standalone) bit.  
> 
>   It looks to me like you may have some command line
> parameter problems,
> or problems with you .ncbirc file.  The data.tar.Z
> file on the ftp site
> contains the scoring matrices, and the tarball
> contains the code.
> 
>   What are you running, including the complete
> command line?
> 
> Joe
> 
> On Wed, 2002-10-09 at 22:05, Bala wrote:
> > Hi All,
> >         I am new to this list,
> > I wondering is it source available
> > for blastall executable from NCBI site.
> > I am getting some error with the one
> > of the parameter(Matrix value) to 
> > blastall.
> > 
> >    If that default file BLOSUM62 is 
> > available locally, then it is working,
> > if I am running from some other location
> > and specifing that file location, then it 
> > is giving error.
> > 
> > [blastall] ERROR: gi|532319|pir|TVFV2E|TVFV2E:
> > BlastKarlinBlkGappedCalc: test/BLOSUM62 is not a
> > supported matrix
> > 
> > any suggestion! help!
> > 
> > -bala-
> > 
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> -- 
> Joseph Landman, Ph.D
> email: landman at scalableinformatics.com
> web  : http://scalableinformatics.com
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> 
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