I want to generate Position Specific Scoring Matrix and later to derive features from it for my application. I am using standalone blast algorithm PSI BLAST to generate PSSM, following are my questions:
- Is it required to use only fasta file as database to construct PSSM?
- Where to find nrdb90 database?
- Suppose we have 1000 sequences in our database than, do we need to construct PSSM with this 1000 sequences all in one file against database using PSI BLAST or do we need to construct separate PSSM for each sequence?