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Open Access Highly Accessed Methodology article

Optimized mixed Markov models for motif identification

Weichun Huang123*, David M Umbach2, Uwe Ohler3 and Leping Li2

Author Affiliations

1 Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA

2 Biostatistics Branch, The National Institute of Environmental Health Sciences, National Institutes of Health, RTP, NC 27709, USA

3 Institute for Genome Sciences & Policy, Duke University Medical Center, Durham, NC 27708, USA

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BMC Bioinformatics 2006, 7:279  doi:10.1186/1471-2105-7-279

Published: 2 June 2006

Additional files

Additional file 1:

The supplement includes the mathematical formulas for computing the probability of a motif site given a Markov model, the algorithmic pseudo-code for the DNJ method, and the description of the parameter estimation for our model. It also contains supplemental materials for the main results as well as other additional results, such as the application for protein domain identification, the comparison of computational time, and so on.

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