Does anyone know why when blastpgp (standalone blast v2.2.1.3) used, PSSM does not created when the input only for one round ( -j 1). But it was created when -j is 2 or above by using the -C option.
I know that the first blast round was the same as the usual Blast, but isn't it should create PSSM by using the homology pair-wise it hit on that search(and Blosum62 matrix of course).
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Narendra Duhita
Waseda University
