Bipartite pattern discovery by entropy minimization-based multiple local alignment

Nucleic Acids Research
Chengpeng Bi, Peter K Rogan

Abstract

Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel bipartite algorithm, bipartite pattern discovery (Bipad), which produces a mathematical model based on information maximization or Shannon's entropy minimization principle, for discovery of bipartite sequence patterns. Bipad is a C++ program that applies greedy methods to search the bipartite alignment space and examines the upstream or downstream regions of co-regulated genes, looking for cis-regulatory bipartite patterns. An input sequence file with zero or one site per locus is required, and the left and right motif widths and a range of possible gap lengths must be specified. Bipad can run in either single-block or bipartite pattern search modes, and it is capable of comprehensively searching all four orientations of half-site patterns. Simulation studies showed that the accuracy of this motif discovery algorithm depends on sample size and motif conservation level, but results were independent of background composition. Bipad performed equivalent with or better than other pattern search algorithms in correctly identifying Escherichia ...Continue Reading

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Citations

Feb 15, 2008·Proceedings of the National Academy of Sciences of the United States of America·Chien-Yu ChenWen-Hsiung Li
May 2, 2007·Bioinformatics·Arijit ChakravartyRobert H Gross
Apr 14, 2011·Nucleic Acids Research·Abha Singh BaisPanayiotis V Benos
Mar 1, 2006·BMC Bioinformatics·Chengpeng Bi, Peter K Rogan
May 10, 2006·PLoS Computational Biology·Kenzie D MacIsaac, Ernest Fraenkel
Mar 19, 2005·Human Mutation·Vijay K Nalla, Peter K Rogan
Nov 28, 2012·Bioorganic & Medicinal Chemistry Letters·Ulf Norinder, Maria E Ek
Jan 25, 2020·Nature Communications·Timothy T HardenJeff Gelles
Dec 14, 2007·Molecular Pharmaceutics·Chengpeng BiCarrie A Vyhlidal

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