Answer to Question #154927 in Bioinformatics for vaibhav

Question #154927

(a) Differentiate between: 1) a standard sequence consensus; 2) a one-dimensional, ‘regular-expression’ motif; 3) a simple, two-dimensional, weight matrix; 4) profile position specific site matrix (PSSM); and 5) a profile Hidden Markov Model (HMM).

Discuss pros and cons, relative power of each, why and when one would be used over the other.

(b) What do logs-odds scoring matrices like the BLOSUM50 table have to do with the concept of ‘pseudocounts’ and background frequencies in most types of multiple sequence alignment profiles?

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