I'm trying to search an NCBI conserved domain against a large genome.
I dowloaded NCBI's CDD PSSM files and indexed the genome both as a
dbtype as well as a
Now I'm trying to run
psi-blast from the command line with one of the PSSM files (CHL00001.smp) against my indexed genome and I'm getting these warnings:
FastaReader: Hyphens are invalid and will be ignored around line 16147 FASTA-Reader: Ignoring invalid residues at position(s): On line 16147: 1, 3-18, 20-22, 25-26, 28-29 FASTA-Reader: Ignoring invalid residues at position(s): On line 16148: 1, 3-4, 6-8, 10, 12-13
And this happens even if I use
I'm assuming the PSSM file is not of the format the blast is accepts (though it seems weird since this PSSM file is from NCBI).