I am a newcomer to ncbi-blast-2.2.29+. Previously, I had been using blastpgp to gain PSSM. In blastpgp, to gain a PSSM of a protein fasta, I ran command as follows:
blastpgp -a $BLAST_NUM_CPUS -t 1 -i $file -j2 -o $id$chain.nr.blast -d NR -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C $id$chain.nr.chk -Q $id$chain.nr.pssm.
Now， What is the best approach to achieve this by ncbi-blast-2.2.29+?
I try it by this command as ./psiblast -query 2KJX.fasta -db nr -out_pssm a.txt -out_ascii_pssm b.pssm, but there does not have any outputs. What am I missing? Any help