question about command-line PSI-BLAST

Martin S geneman at stanford.edu
Tue Jun 17 09:34:26 EST 2003


Thanks for the quick reply

I tried saving in both DOS format and converting to unix format 
(removing the \r character from the \r\n termination) and obtain the 
same error with both unix and DOS formatted files.

I reran the Unix formatted files on a machine running Redhat 7.3 at home 
and got blastpgp and blastall (psitblastn) to work.  It seems that this 
is only a Windows blastpgp related problem

-Martin


Aaron J Mackey wrote:
> On 9 Jun 2003, Martin S wrote:
> 
> 
>>..\blastpgp -i seq1.fasta -B align1.aln -j 1 -d somedatabase.fasta
>>
>>And I get:
>>
>>[NULL_Caption] WARNING:
>>Invalid character or wrong number of characters in sequence index 30
>>[NULL_Caption] WARNING:
>>None of the alignment sequences equals the query sequence
>>[NULL_Caption] WARNING:
>>Cannot recover alignment checkpoint
> 
> 
> It looks like your align1.aln isn't being read properly; does it have DOS
> newlines, or UNIX newlines?
> 
> 
>>Besides getting psiblast to work, I'm also wondering if there is there a
>>way to get the PSSM files obtained from semi-automated PSI-BLAST (on the
>>ncbi servers) to work on command-line PSI-BLAST
> 
> 
> At least the last time I checked a few months ago, the answer is no; the
> PSSM file that you get from the website is a human-readable text version;
> the PSSM checkpoint files you can use with the command line -R option are
> a binary format (written via command line -C option) which I don't believe
> you can get via the web site.
> 
> Best of luck,
> 
> -Aaron
> 





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