question about command-line PSI-BLAST

Aaron J Mackey ajm6q at virginia.edu
Tue Jun 10 04:15:31 EST 2003

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 J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu

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