Maximum Discrimination Hidden Markov Models of Sequence Consensus
- 1 January 1995
- journal article
- research article
- Published by Mary Ann Liebert Inc in Journal of Computational Biology
- Vol. 2 (1), 9-23
- https://doi.org/10.1089/cmb.1995.2.9
Abstract
We introduce a maximum discrimination method for building hidden Markov models (HMMs) of protein or nucleic acid primary sequence consensus. The method compensates for biased representation in sequence data sets, superseding the need for sequence weighting methods. Maximum discrimination HMMs are more sensitive for detecting distant sequence homologs than various other HMM methods or BLAST when tested on globin and protein kinase catalytic domain sequences. Key words: hidden Markov model; database searching; sequence consensus; sequence weightingKeywords
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