{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T07:15:44Z","timestamp":1761894944397},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Discovering cis-regulatory elements in genome sequence remains a challenging issue. Several methods rely on the optimization of some target scoring function. The information content (IC) or relative entropy of the motif has proven to be a good estimator of transcription factor DNA binding affinity. However, these information-based metrics are usually used as a posteriori statistics rather than during the motif search process itself.<\/jats:p>\n               <jats:p>Results: We introduce here info-gibbs, a Gibbs sampling algorithm that efficiently optimizes the IC or the log-likelihood ratio (LLR) of the motif while keeping computation time low. The method compares well with existing methods like MEME, BioProspector, Gibbs or GAME on both synthetic and biological datasets. Our study shows that motif discovery techniques can be enhanced by directly focusing the search on the motif IC or the motif LLR.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/rsat.ulb.ac.be\/rsat\/info-gibbs<\/jats:p>\n               <jats:p>Contact: \u00a0defrance@bigre.ulb.ac.be<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp490","type":"journal-article","created":{"date-parts":[[2009,8,19]],"date-time":"2009-08-19T03:03:10Z","timestamp":1250650990000},"page":"2715-2722","source":"Crossref","is-referenced-by-count":24,"title":["info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling"],"prefix":"10.1093","volume":"25","author":[{"given":"Matthieu","family":"Defrance","sequence":"first","affiliation":[{"name":"Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, B-1050 Bruxelles, Belgium"}]},{"given":"Jacques","family":"van Helden","sequence":"additional","affiliation":[{"name":"Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, B-1050 Bruxelles, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2009,8,18]]},"reference":[{"key":"2023013112130092300_B1","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","volume":"2","author":"Bailey","year":"1994","journal-title":"Proc. Inter. Conf. Intell. Syst. Mol. Biol."},{"key":"2023013112130092300_B2","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1093\/bioinformatics\/btm606","article-title":"TFBS identification based on genetic algorithm with combined representations and adaptive post-processing","volume":"24","author":"Chan","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112130092300_B3","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res."},{"key":"2023013112130092300_B4","doi-asserted-by":"crossref","first-page":"D120","DOI":"10.1093\/nar\/gkm994","article-title":"RegulonDB (version 6.0): gene regulation model of Escherichia coli k-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation","volume":"36","author":"Gama-Castro","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112130092300_B5","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nature02800","article-title":"Transcriptional regulatory code of a eukaryotic genome","volume":"431","author":"Harbison","year":"2004","journal-title":"Nature"},{"key":"2023013112130092300_B6","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1093\/bioinformatics\/15.7.563","article-title":"Identifying dna and protein patterns with statistically significant alignments of multiple sequences","volume":"15","author":"Hertz","year":"1999","journal-title":"Bioinformatics"},{"key":"2023013112130092300_B7","first-page":"81","article-title":"Identification of consensus patterns in unaligned dna sequences known to be functionally related","volume":"6","author":"Hertz","year":"1990","journal-title":"Comput. Appl. Biosci."},{"key":"2023013112130092300_B8","doi-asserted-by":"crossref","first-page":"1205","DOI":"10.1006\/jmbi.2000.3519","article-title":"Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae","volume":"296","author":"Hughes","year":"2000","journal-title":"J. Mol. Biol."},{"key":"2023013112130092300_B9","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1214\/088342304000000107","article-title":"Computational discovery of gene regulatory binding motifs: a bayesian perspective","volume":"19","author":"Jensen","year":"2004","journal-title":"Stat. Sci."},{"key":"2023013112130092300_B10","doi-asserted-by":"crossref","first-page":"1557","DOI":"10.1093\/bioinformatics\/bth127","article-title":"Biooptimizer: a Bayesian scoring function approach to motif discovery","volume":"20","author":"Jensen","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013112130092300_B11","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1126\/science.8211139","article-title":"Detecting subtle sequence signals: a gibbs sampling strategy for multiple alignment","volume":"262","author":"Lawrence","year":"1993","journal-title":"Science"},{"key":"2023013112130092300_B12","doi-asserted-by":"crossref","first-page":"1156","DOI":"10.1080\/01621459.1995.10476622","article-title":"Bayesian models for multiple local sequence alignment and Gibbs sampling strategies","volume":"90","author":"Liu","year":"1995","journal-title":"J. Am. Stat. Assoc."},{"key":"2023013112130092300_B13","first-page":"127","article-title":"BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes","volume":"6","author":"Liu","year":"2001","journal-title":"Pacific Symposium on Biocomputing"},{"key":"2023013112130092300_B14","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.1002\/pro.5560040820","article-title":"Gibbs motif sampling: detection of bacterial outer membrane protein repeats","volume":"4","author":"Neuwald","year":"1995","journal-title":"Protein Sci."},{"key":"2023013112130092300_B15","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1093\/bioinformatics\/btm610","article-title":"Natural similarity measures between position frequency matrices with an application to clustering","volume":"24","author":"Pape","year":"2008","journal-title":"Bioinformatics"},{"issue":"Suppl. 1","key":"2023013112130092300_B16","doi-asserted-by":"crossref","first-page":"S207","DOI":"10.1093\/bioinformatics\/17.suppl_1.S207","article-title":"An algorithm for finding signals of unknown length in DNA sequences","volume":"17","author":"Pavesi","year":"2001","journal-title":"Bioinformatics"},{"key":"2023013112130092300_B17","first-page":"269","article-title":"Combinatorial approaches to finding subtle signals in DNA sequences","volume":"8","author":"Pevzner","year":"2000","journal-title":"Proc. Inter. Conf. Intell. Syst. Mol. Biol."},{"key":"2023013112130092300_B18","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1038\/nbt1098-939","article-title":"Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation","volume":"16","author":"Roth","year":"1998","journal-title":"Nat. Biotechnol."},{"key":"2023013112130092300_B19","doi-asserted-by":"crossref","first-page":"6097","DOI":"10.1093\/nar\/18.20.6097","article-title":"Sequence logos: a new way to display consensus sequences","volume":"18","author":"Schneider","year":"1990","journal-title":"Nucleic Acids Res."},{"key":"2023013112130092300_B20","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/0022-2836(86)90165-8","article-title":"Information content of binding sites on nucleotide sequences","volume":"188","author":"Schneider","year":"1986","journal-title":"J. Mol. Biol."},{"key":"2023013112130092300_B21","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1186\/1471-2105-7-486","article-title":"Gibbsst: a Gibbs sampling method for motif discovery with enhanced resistance to local optima","volume":"7","author":"Shida","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013112130092300_B22","first-page":"3","article-title":"Hybrid Gibbs-sampling algorithm for challenging motif discovery: Gibbsdst","volume":"17","author":"Shida","year":"2006","journal-title":"Genome Inform."},{"key":"2023013112130092300_B23","doi-asserted-by":"crossref","first-page":"5549","DOI":"10.1093\/nar\/gkf669","article-title":"Discovery of novel transcription factor binding sites by statistical overrepresentation","volume":"30","author":"Sinha","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023013112130092300_B24","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1093\/nar\/gkg618","article-title":"YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation","volume":"31","author":"Sinha","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023013112130092300_B25","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1006\/jtbi.1998.0785","article-title":"Information content and free energy in DNA\u2013protein interactions","volume":"195","author":"Stormo","year":"1998","journal-title":"J. Theor. Biol."},{"key":"2023013112130092300_B26","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1093\/bioinformatics\/17.12.1113","article-title":"A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling","volume":"17","author":"Thijs","year":"2001","journal-title":"Bioinformatics"},{"key":"2023013112130092300_B27","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1089\/10665270252935566","article-title":"A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes","volume":"9","author":"Thijs","year":"2002","journal-title":"J. Comput. Biol."},{"key":"2023013112130092300_B28","doi-asserted-by":"crossref","first-page":"W119","DOI":"10.1093\/nar\/gkn304","article-title":"RSAT: regulatory sequence analysis tools","volume":"36","author":"Thomas-Chollier","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112130092300_B29","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/nbt1053","article-title":"Assessing computational tools for the discovery of transcription factor binding sites","volume":"23","author":"Tompa","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2023013112130092300_B30","doi-asserted-by":"crossref","first-page":"3593","DOI":"10.1093\/nar\/gkg567","article-title":"Regulatory sequence analysis tools","volume":"31","author":"van Helden","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023013112130092300_B31","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1006\/jmbi.1998.1947","article-title":"Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies","volume":"281","author":"van Helden","year":"1998","journal-title":"J. Mol. Biol."},{"key":"2023013112130092300_B32","doi-asserted-by":"crossref","first-page":"1808","DOI":"10.1093\/nar\/28.8.1808","article-title":"Discovering regulatory elements in non-coding sequences by analysis of spaced dyads","volume":"28","author":"van Helden","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023013112130092300_B33","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1093\/bioinformatics\/btl147","article-title":"Game: detecting cis-regulatory elements using a genetic algorithm","volume":"22","author":"Wei","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013112130092300_B34","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1093\/bioinformatics\/15.7.607","article-title":"SCPD: a promoter database of the yeast Saccharomyces cerevisiae","volume":"15","author":"Zhu","year":"1999","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/20\/2715\/48993723\/bioinformatics_25_20_2715.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/20\/2715\/48993723\/bioinformatics_25_20_2715.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:40:19Z","timestamp":1675201219000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/20\/2715\/193858"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,8,18]]},"references-count":34,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2009,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp490","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,10,15]]},"published":{"date-parts":[[2009,8,18]]}}}