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