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Comparative and Functional Genomics
Volume 4, Issue 2, Pages 250-254
Conference Review

Specialized Hidden Markov Model Databases for Microbial Genomics

University of Nevada, Reno, 1664 N. Virginia Street, Reno 89557-0014, NV, USA

Received 27 January 2003; Revised 5 February 2003; Accepted 6 February 2003

Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


As hidden Markov models (HMMs) become increasingly more important in the analysis of biological sequences, so too have databases of HMMs expanded in size, number and importance. While the standard paradigm a short while ago was the analysis of one or a few sequences at a time, it has now become standard procedure to submit an entire microbial genome. In the future, it will be common to submit large groups of completed genomes to run simultaneously against a dozen public databases and any number of internally developed targets. This paper looks at some of the readily available HMM (or HMM-like) algorithms and several publicly available HMM databases, and outlines methods by which the reader may develop custom HMM targets.