Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware

T. Oliver; Bertil Schmidt; Y. Jakop; Douglas Leslie Maskell

doi:10.1007/11758501_71

Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware

In: Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware (Lecture notes in computer science)

Chapter In A Book 2006 English

Abstract

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Profile Hidden Markov Models (PHMMs) are used as a popular tool in bioinformatics for probabilistic sequence database searching. The search operation consists of computing the Viterbi score for each sequence in the database with respect to a given query PHMM. Because...

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