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Bioinformatics Advance Access published online on July 10, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm350
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

HMMoC – a compiler for hidden Markov models

Gerton Lunter *,1

1Unit, Dept. of Physiology, Anatomy and Genetics, South Parks Road, OX1 3TG, University of Oxford.

*To whom correspondence should be addressed. Gerton Lunter, E-mail: gerton.lunter{at}dpag.ox.ac.uk


  Abstract

Summary:Hidden Markov models are widely applied within computational biology. The large datasets and complex models involved demand optimized implementations, while efficient exploration of model space requires rapid prototyping. These requirements are not met by existing solutions, and hand-coding is time-consuming and error-prone. Here, I present a compiler that takes over the mechanical process of implementing HMM algorithms, by translating high-level XML descriptions into efficient C++ implementations. The compiler is highly customizable, produces efficient and bug-free code, and includes several optimizations.

Availability:http://genserv.anat.ox.ac.uk/software

Contact: gerton.lunter{at}dpag.ox.ac.uk

Associate Editor: Dr. Alex Bateman

Received on May 30, 2007; revised on June 26, 2007; accepted on June 27, 2007

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