Computational Biology of Transcription Factor Binding

Volume 674 of the series Methods in Molecular Biology pp 85-95


Motif Discovery Using Expectation Maximization and Gibbs’ Sampling

  • Gary D. StormoAffiliated withDepartment of Genetics, School of Medicine, Washington University Email author 

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Expectation maximization and Gibbs’ sampling are two statistical approaches used to identify transcription factor binding sites and the motif that represents them. Both take as input unaligned sequences and search for a statistically significant alignment of putative binding sites. Expectation maximization is deterministic so that starting with the same initial parameters will always converge to the same solution, making it wise to start it multiple times from different initial parameters. Gibbs’ sampling is stochastic so that it may arrive at different solutions from the same initial parameters. In both cases multiple runs are advised because comparisons of the solutions after each run can indicate whether a global, optimum solution is likely to have been achieved.

Key words

Expectation maximization Gibbs’ sampling transcription factor binding sites motif discovery position weight matrices position frequency matrices regulatory sites motif modeling