PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.

PhyloGibbs, our recent Gibbs-sampling motif-finder, takes phylogeny into account in detecting binding sites for transcription factors in DNA and assigns posterior probabilities to its predictions obtained by sampling the entire configuration space. Here, in an extension called PhyloGibbs-MP, we wide...

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Autor principal:	Rahul Siddharthan
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/c45d4b4f5375441895f11e3c06cbda34
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spelling	oai:doaj.org-article:c45d4b4f5375441895f11e3c06cbda342021-11-25T05:41:59ZPhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.1553-734X1553-735810.1371/journal.pcbi.1000156https://doaj.org/article/c45d4b4f5375441895f11e3c06cbda342008-08-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18769735/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358PhyloGibbs, our recent Gibbs-sampling motif-finder, takes phylogeny into account in detecting binding sites for transcription factors in DNA and assigns posterior probabilities to its predictions obtained by sampling the entire configuration space. Here, in an extension called PhyloGibbs-MP, we widen the scope of the program, addressing two major problems in computational regulatory genomics. First, PhyloGibbs-MP can localise predictions to small, undetermined regions of a large input sequence, thus effectively predicting cis-regulatory modules (CRMs) ab initio while simultaneously predicting binding sites in those modules-tasks that are usually done by two separate programs. PhyloGibbs-MP's performance at such ab initio CRM prediction is comparable with or superior to dedicated module-prediction software that use prior knowledge of previously characterised transcription factors. Second, PhyloGibbs-MP can predict motifs that differentiate between two (or more) different groups of regulatory regions, that is, motifs that occur preferentially in one group over the others. While other "discriminative motif-finders" have been published in the literature, PhyloGibbs-MP's implementation has some unique features and flexibility. Benchmarks on synthetic and actual genomic data show that this algorithm is successful at enhancing predictions of differentiating sites and suppressing predictions of common sites and compares with or outperforms other discriminative motif-finders on actual genomic data. Additional enhancements include significant performance and speed improvements, the ability to use "informative priors" on known transcription factors, and the ability to output annotations in a format that can be visualised with the Generic Genome Browser. In stand-alone motif-finding, PhyloGibbs-MP remains competitive, outperforming PhyloGibbs-1.0 and other programs on benchmark data.Rahul SiddharthanPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 4, Iss 8, p e1000156 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Rahul Siddharthan PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.
description	PhyloGibbs, our recent Gibbs-sampling motif-finder, takes phylogeny into account in detecting binding sites for transcription factors in DNA and assigns posterior probabilities to its predictions obtained by sampling the entire configuration space. Here, in an extension called PhyloGibbs-MP, we widen the scope of the program, addressing two major problems in computational regulatory genomics. First, PhyloGibbs-MP can localise predictions to small, undetermined regions of a large input sequence, thus effectively predicting cis-regulatory modules (CRMs) ab initio while simultaneously predicting binding sites in those modules-tasks that are usually done by two separate programs. PhyloGibbs-MP's performance at such ab initio CRM prediction is comparable with or superior to dedicated module-prediction software that use prior knowledge of previously characterised transcription factors. Second, PhyloGibbs-MP can predict motifs that differentiate between two (or more) different groups of regulatory regions, that is, motifs that occur preferentially in one group over the others. While other "discriminative motif-finders" have been published in the literature, PhyloGibbs-MP's implementation has some unique features and flexibility. Benchmarks on synthetic and actual genomic data show that this algorithm is successful at enhancing predictions of differentiating sites and suppressing predictions of common sites and compares with or outperforms other discriminative motif-finders on actual genomic data. Additional enhancements include significant performance and speed improvements, the ability to use "informative priors" on known transcription factors, and the ability to output annotations in a format that can be visualised with the Generic Genome Browser. In stand-alone motif-finding, PhyloGibbs-MP remains competitive, outperforming PhyloGibbs-1.0 and other programs on benchmark data.
format	article
author	Rahul Siddharthan
author_facet	Rahul Siddharthan
author_sort	Rahul Siddharthan
title	PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.
title_short	PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.
title_full	PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.
title_fullStr	PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.
title_full_unstemmed	PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.
title_sort	phylogibbs-mp: module prediction and discriminative motif-finding by gibbs sampling.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/c45d4b4f5375441895f11e3c06cbda34
work_keys_str_mv	AT rahulsiddharthan phylogibbsmpmodulepredictionanddiscriminativemotiffindingbygibbssampling
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PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling.

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