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{"ops":[{"insert":"(a) Differentiate between: 1) a standard sequence consensus; 2) a one-dimensional, \u2018regular-expression\u2019 motif; 3) a simple, two-dimensional, weight matrix; 4) profile position specific site matrix (PSSM); and 5) a profile Hidden Markov Model (HMM).\nDiscuss pros and cons, relative power of each, why and when one would be used over the other.\n(b) What do logs-odds scoring matrices like the BLOSUM50 table have to do with the concept of \u2018pseudocounts\u2019 and background frequencies in most types of multiple sequence alignment profiles?\n"}]}
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