At the core of the HMMER search is the Viterbi algorithm, used to compute the most probable path through a given state model. Algorithm 3 shows the pseudocode for a typical HMMER database search, and listing 1 provides a code snippet of the most time consuming portion of the P7Viterbi algorithm.
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EXPLORING LONG-RANGE FEATURES IN BIOSEQUENCES FOR STRUCTURE AND INTERACTION PREDICTION by Colin Kern Approved: Errol Lloyd, Ph.D. Chair of the Department of Computer & Information Sciences
Feb 21, 2019 · Viterbi Algorithm: We will be using a much more efficient algorithm named Viterbi Algorithm to solve the decoding problem. So far in HMM we went deep into deriving equations for all the algorithms in order to understand them clearly. However Viterbi Algorithm is best understood using an analytical example rather than equations.