V. Fonzo, F. Aluffi-Pentini, V. Parisi
tlooto Summary
This survey considers the major bioinformatics applications ofHidden Markov Models, such as alignment, labeling, and profiling of sequences, protein structure prediction, and pattern recognition, and provides a critical appraisal of the use and perspectives of HMMs.
Abstract
Hidden Markov Models (HMMs) became recently important and popular among bioinformatics researchers, and many software tools are based on them. In this survey, we first consider in some detail the mathematical foundations of HMMs, we describe the most important algorithms, and provide useful comparisons, pointing out advantages and drawbacks. We then consider the major bioinformatics applications, such as alignment, labeling, and profiling of sequences, protein structure prediction, and pattern recognition. We finally provide a critical appraisal of the use and perspectives of HMMs in bioinformatics.
Citation format
FONZO, V.; ALUFFI-PENTINI, F.; PARISI, V. Hidden markov models in bioinformatics. Current Bioinformatics, 2007, 2: 49–61.