<p>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.</p> <p>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.</p>
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Comp Funct Genomics. 2003 Apr; 4(2):250-254