[BiO BB] makemat cannot open the profile file?

Gary Van Domselaar gary at www.bioinformatics.org
Tue Apr 19 09:48:02 EDT 2005


Hi Magda,

Although I am no expert on PSIBLAST, I do recall seeing 'psipred' use the
following code with sucess:

<snip>
$ncbidir/blastpgp -b 0 -j 3 -h 0.001 -d $dbname -i psitmp.fasta -C 
psitmp.chk >&
 $rootname.blast

echo psitmp.chk > psitmp.pn
echo psitmp.fasta > psitmp.sn
$ncbidir/makemat -P psitmp
</snip>

so I assume you need to have a common rootname and appropriate '.pn' and
'.sn' extensions for your matrix file and fasta file, respectfully, and 
then call makemat on the rootname.

Best of Luck,

g.
--
Gary Van Domselaar, Ph.D.
gary at bioinformatics.org





On Tue, 19 Apr 2005, Magda Mansour wrote:

> Hello,
> 
> I'm a computer engineer student and currently working
> on a bioinformatics project using PSI-BLAST. I'm
> completely new in this domain and I have a little
> problem with the PSI-BLAST function "makemat".
> 
> I first created a profile using blastpgp:
> blastpgp -d dataBase\nr -i files\protein.txt -o
> files\protein.out -C data\matrix –j 3
> 
> Then using the function makemat to create an ASCII
> file from this matrix file with:
> makemat -d DataBase\nr -P data\matrix
> It gives me the error:
> [NULL_Caption] FATAL ERROR: Unable to open file ||@
> 
> I tried to construct this same matrix with different
> extensions: bin, chk, sn, mn, aux...
> It gives me the output:
> [NULL_Caption] FATAL ERROR: Unable to open profiles
> file data\matrix.ext.pn
> I did not found on Internet a documentation on the pn
> extension.
> 
> Although, working with this matrix for a new iteration
> worked properly:
> blastpgp -d dataBase\nr -i files\protein.txt -o
> files\protein.out -R data\matrix
> 
> If somebody can help me on this point I would be very
> grateful,
> 
> Sincerely, 
> Yours,
> Magda Mansour
> 
> 
> 	
> 
> 	
> 		
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