{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T04:14:51Z","timestamp":1728360891218},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,4,4]],"date-time":"2005-04-04T00:00:00Z","timestamp":1112572800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,4,4]],"date-time":"2005-04-04T00:00:00Z","timestamp":1112572800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>Transcription factor binding site (TFBS) prediction is a difficult problem, which requires a good scoring function to discriminate between real binding sites and background noise. Many scoring functions have been proposed in the literature, but it is difficult to assess their relative performance, because they are implemented in different software tools using different search methods and different TFBS representations.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>Here we compare how several scoring functions perform on both real and semi-simulated data sets in a common test environment. We have also developed two new scoring functions and included them in the comparison. The data sets are from the yeast (<jats:italic>S. cerevisiae<\/jats:italic>) genome.<\/jats:p>\n                        <jats:p>Our new scoring function LLBG (least likely under the background model) performs best in this study. It achieves the best average rank for the correct motifs. Scoring functions based on positional bias performed quite poorly in this study.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>LLBG may provide an interesting alternative to current scoring functions for TFBS prediction.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-6-84","type":"journal-article","created":{"date-parts":[[2005,4,5]],"date-time":"2005-04-05T06:13:42Z","timestamp":1112681622000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Scoring functions for transcription factor binding site prediction"],"prefix":"10.1186","volume":"6","author":[{"given":"Markus","family":"Friberg","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"von Rohr","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gaston","family":"Gonnet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,4,4]]},"reference":[{"key":"409_CR1","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1186\/gb-2003-5-1-201","volume":"5","author":"ML Bulyk","year":"2003","unstructured":"Bulyk ML: Computational prediction of transcription-factor binding site locations. Genome Biol 2003, 5: 201. 10.1186\/gb-2003-5-1-201","journal-title":"Genome Biol"},{"key":"409_CR2","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1093\/bib\/5.3.217","volume":"5","author":"G Pavesi","year":"2004","unstructured":"Pavesi G, Mauri G, Pesole G: In silico representation and discovery of transcription factor binding sites. Brief Bioinform 2004, 5: 217\u2013236.","journal-title":"Brief Bioinform"},{"key":"409_CR3","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1093\/bioinformatics\/15.7.563","volume":"15","author":"GZ Hertz","year":"1999","unstructured":"Hertz GZ, Stormo GD: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15: 563\u2013577. 10.1093\/bioinformatics\/15.7.563","journal-title":"Bioinformatics"},{"key":"409_CR4","first-page":"28","volume":"2","author":"TL Bailey","year":"1994","unstructured":"Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2: 28\u201336.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"409_CR5","first-page":"21","volume":"3","author":"TL Bailey","year":"1995","unstructured":"Bailey TL, Elkan C: The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 1995, 3: 21\u201329.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"409_CR6","doi-asserted-by":"publisher","first-page":"1205","DOI":"10.1006\/jmbi.2000.3519","volume":"296","author":"JD Hughes","year":"2000","unstructured":"Hughes JD, Estep PW, Tavazoie S, Church GM: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296: 1205\u20131214. 10.1006\/jmbi.2000.3519","journal-title":"J Mol Biol"},{"key":"409_CR7","first-page":"127","volume-title":"Pac Symp Biocomput","author":"X Liu","year":"2001","unstructured":"Liu X, Brutlag DL, Liu JS: BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 2001, 127\u2013138."},{"key":"409_CR8","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1038\/nbt717","volume":"20","author":"XS Liu","year":"2002","unstructured":"Liu XS, Brutlag DL, Liu JS: An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 2002, 20: 835\u2013839.","journal-title":"Nat Biotechnol"},{"key":"409_CR9","doi-asserted-by":"publisher","first-page":"1808","DOI":"10.1093\/nar\/28.8.1808","volume":"28","author":"J van Helden","year":"2000","unstructured":"van Helden J, Rios AF, Collado-Vides J: Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res 2000, 28: 1808\u20131818. 10.1093\/nar\/28.8.1808","journal-title":"Nucleic Acids Res"},{"issue":"Suppl 2","key":"409_CR10","doi-asserted-by":"publisher","first-page":"II149","DOI":"10.1093\/bioinformatics\/btg1072","volume":"19","author":"A Price","year":"2003","unstructured":"Price A, Ramabhadran S, Pevzner PA: Finding subtle motifs by branching from sample strings. Bioinformatics 2003, 19(Suppl 2):II149-II155.","journal-title":"Bioinformatics"},{"key":"409_CR11","volume-title":"Proc Seventh Annual Inter Conf on Computational Molecular Biology (RECOMB)","author":"Y Barash","year":"2003","unstructured":"Barash Y, Elidan G, Friedman N, Kaplan T: Modeling Dependencies in Protein-DNA Binding Sites. Proc Seventh Annual Inter Conf on Computational Molecular Biology (RECOMB) 2003."},{"key":"409_CR12","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1093\/bioinformatics\/14.4.317","volume":"14","author":"T Yada","year":"1998","unstructured":"Yada T, Totoki Y, Ishikawa M, Asai K, Nakai K: Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinformatics 1998, 14: 317\u2013325. 10.1093\/bioinformatics\/14.4.317","journal-title":"Bioinformatics"},{"key":"409_CR13","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1126\/science.8211139","volume":"262","author":"CE Lawrence","year":"1993","unstructured":"Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC: Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262: 208\u2013214.","journal-title":"Science"},{"key":"409_CR14","doi-asserted-by":"publisher","first-page":"1952","DOI":"10.1093\/bioinformatics\/btg266","volume":"19","author":"C Narasimhan","year":"2003","unstructured":"Narasimhan C, LoCascio P, Uberbacher E: Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection. Bioinformatics 2003, 19: 1952\u20131963. 10.1093\/bioinformatics\/btg266","journal-title":"Bioinformatics"},{"key":"409_CR15","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/1477-5956-2-3","volume":"2","author":"A Hoglund","year":"2004","unstructured":"Hoglund A, Kohlbacher O: From sequence to structure and back again: approaches for predicting protein-DNA binding. Proteome Sci 2004, 2: 3. 10.1186\/1477-5956-2-3","journal-title":"Proteome Sci"},{"key":"409_CR16","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1101\/gr.2080004","volume":"14","author":"H Wang","year":"2004","unstructured":"Wang H, Noordewier M, Benham CJ: Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters. Genome Res 2004, 14: 1575\u20131584. 10.1101\/gr.2080004","journal-title":"Genome Res"},{"key":"409_CR17","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1126\/science.1063127","volume":"293","author":"T Jenuwein","year":"2001","unstructured":"Jenuwein T, Allis CD: Translating the histone code. Science 2001, 293: 1074\u20131080. 10.1126\/science.1063127","journal-title":"Science"},{"key":"409_CR18","doi-asserted-by":"publisher","first-page":"4442","DOI":"10.1093\/nar\/gkf578","volume":"30","author":"PV Benos","year":"2002","unstructured":"Benos PV, Bulyk ML, Stormo GD: Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res 2002, 30: 4442\u20134451. 10.1093\/nar\/gkf578","journal-title":"Nucleic Acids Res"},{"issue":"Suppl 1","key":"409_CR19","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1093\/bioinformatics\/bth927","volume":"20","author":"MJ De Hoon","year":"2004","unstructured":"De Hoon MJ, Makita Y, Imoto S, Kobayashi K, Ogasawara N, Nakai K, Miyano S: Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. Bioinformatics 2004, 20(Suppl 1):101\u2013108. 10.1093\/bioinformatics\/bth927","journal-title":"Bioinformatics"},{"key":"409_CR20","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1093\/bioinformatics\/15.7.607","volume":"15","author":"J Zhu","year":"1999","unstructured":"Zhu J, Zhang MQ: SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 1999, 15: 607\u2013611. 10.1093\/bioinformatics\/15.7.607","journal-title":"Bioinformatics"},{"key":"409_CR21","doi-asserted-by":"publisher","first-page":"32310","DOI":"10.1074\/jbc.M005946200","volume":"275","author":"C Gross","year":"2000","unstructured":"Gross C, Kelleher M, Iyer VR, Brown PO, Winge DR: Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays. J Biol Chem 2000, 275: 32310\u201332316. 10.1074\/jbc.M005946200","journal-title":"J Biol Chem"},{"issue":"Pt 1","key":"409_CR22","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1099\/00221287-144-1-13","volume":"144","author":"CJ Klein","year":"1998","unstructured":"Klein CJ, Olsson L, Nielsen J: Glucose control in Saccharomyces cerevisiae: the role of Mig1 in metabolic functions. Microbiology 1998, 144(Pt 1):13\u201324.","journal-title":"Microbiology"},{"key":"409_CR23","first-page":"151","volume-title":"Pac Symp Biocomput","author":"P Pavlidis","year":"2001","unstructured":"Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN: Promoter region-based classification of genes. Pac Symp Biocomput 2001, 151\u2013163."},{"key":"409_CR24","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1093\/bioinformatics\/15.4.267","volume":"15","author":"RF Lascaris","year":"1999","unstructured":"Lascaris RF, Mager WH, Planta RJ: DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences. Bioinformatics 1999, 15: 267\u2013277. 10.1093\/bioinformatics\/15.4.267","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-84.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-84\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-84.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:10:12Z","timestamp":1728303012000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-84"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,4,4]]},"references-count":24,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["409"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-84","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2005,4,4]]},"assertion":[{"value":"12 November 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 April 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 April 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"84"}}