Algorithms for phylogenetic footprinting
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Enhanced position weight matrices using mixture models
Bioinformatics
Monte Carlo Strategies in Scientific Computing
Monte Carlo Strategies in Scientific Computing
PhyloGibbs: a gibbs sampler incorporating phylogenetic information
RRG'04 Proceedings of the 2004 RECOMB international conference on Regulatory Genomics
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In phylogenetic foot-printing, putative regulatory elements are found in upstream regions of orthologous genes by searching for common motifs. Motifs in different upstream sequences are subject to mutations along the edges of the corresponding phylogenetic tree, consequently taking advantage of the tree in the motif search is an appealing idea. We describe the Motif Yggdrasil sampler; the first Gibbs sampler based on a general tree that uses unaligned sequences. Previous tree-based Gibbs samplers have assumed a star-shaped tree or partially aligned upstream regions. We give a probabilistic model describing upstream sequences with regulatory elements and build a Gibbs sampler with respect to this model. We apply the collapsing technique to eliminate the need to sample nuisance parameters, and give a derivation of the predictive update formula. The use of the tree achieves a substantial increase in nucleotide level correlation coefficient both for synthetic data and 37 bacterial lexA genes.