PSI BLAST to create PSSM with BLAST+

Question

[farberak]

I would like to generate PSSM in blast+. I can run the program and I have required databases downloaded in my computer (nr protein data). What are the necessary steps and commands.

Thank you

Answer 1

[sanrrone]

just execute the command psiblast -query myfasta.fasta -db mydb -num_iterations 3 -out_pssm mypssm.smp