I'm able to generate a PSSM and a sequence from combinatorial experimental data. I want to BLAST the results to find proteins displaying these motifs. However, I have information about each position's sensitivity to substitutions, in addition to a consensus sequence. I know how to create a PSSM from this information, but I don't know how to incorporate this into a BLAST search. Does anyone know a cmdline argument to blast or a way of hacking a PSSM into a PSI-BLAST search to add position information to a sequence?
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