[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:

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

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

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,

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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