{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,6]],"date-time":"2023-02-06T22:52:35Z","timestamp":1675723955774},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Many gene identification methods assign scores to gene elements prior to their assembly into predicted genes. The scoring system is often based on log-likelihood ratios. These methods usually perform well but it is difficult to interpret how significant a score is.<\/jats:p>\n               <jats:p>Results: We have developed several tests of significance for the scores: (1) a sum-of-scores test (SST), (2) an intersection-union test (IUT), based on a multiple hypothesis testing interpretation of an exon's score and (3) a meta-analytical approach (MA), which combines several P-values, corresponding to the exon's parts, to yield a global P-value. We performed simulation studies, which show that the MA has better sensitivity and specificity than other methods and is easier to interpret by non-expert users. This is an improvement over other methods and is especially relevant for users who would like to predict incomplete gene sequences.<\/jats:p>\n               <jats:p>Contact: \u00a0asanchez@ub.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl544","type":"journal-article","created":{"date-parts":[[2006,10,26]],"date-time":"2006-10-26T00:17:34Z","timestamp":1161821854000},"page":"3003-3008","source":"Crossref","is-referenced-by-count":2,"title":["Hypothesis testing approaches to the exon prediction problem"],"prefix":"10.1093","volume":"22","author":[{"given":"Mireia","family":"Vilardell","sequence":"first","affiliation":[{"name":"Statistics Department, University of Barcelona 1 \u00a0 1 \u00a0 \u00a0 Barcelona, Spain"},{"name":"Genetics Unit, Department of Experimental and Health Sciences, Pompeu Fabra University 2 \u00a0 2 \u00a0 \u00a0 Barcelona, Spain"}]},{"given":"Alex","family":"S\u00e1nchez-Pla","sequence":"additional","affiliation":[{"name":"Statistics Department, University of Barcelona 1 \u00a0 1 \u00a0 \u00a0 Barcelona, Spain"}]}],"member":"286","published-online":{"date-parts":[[2006,5,18]]},"reference":[{"key":"2023012408503367800_b1","first-page":"191","article-title":"Scoring Hidden Markov Models","volume":"13","author":"Barrett","year":"1997","journal-title":"Comput. Appl. Biosci. Apr."},{"key":"2023012408503367800_b2","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","article-title":"Prediction of complete gene structures in human genomic DNA","volume":"268","author":"Burge","year":"1997","journal-title":"J. Mol. Biol."},{"key":"2023012408503367800_b3","volume-title":"Statistical Inference","author":"Casella","year":"2002","edition":"2nd edn"},{"key":"2023012408503367800_b4","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-3247-4","volume-title":"Statistical Methods in Bioinformatics: An Introduction","author":"Ewans","year":"2001"},{"key":"2023012408503367800_b5","author":"Green","year":"2001"},{"key":"2023012408503367800_b6","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1007\/s001099770003","article-title":"Computational gene identification","volume":"75","author":"Guig\u00f3","year":"1997","journal-title":"J. Mol. Med."},{"key":"2023012408503367800_b7","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1101\/gr.122800","article-title":"An assessment of gene prediction accuracy in large DNA sequences","volume":"10","author":"Guig\u00f3","year":"2000","journal-title":"Genome Res."},{"key":"2023012408503367800_b8","volume-title":"Statistical Methods for Meta-Analysis","author":"Hedges","year":"1985"},{"key":"2023012408503367800_b9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1089\/106652704773416858","article-title":"Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification","volume":"11","author":"Huang","year":"2004","journal-title":"J. Comput. Biol."},{"key":"2023012408503367800_b10","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1101\/gr.10.4.511","article-title":"geneid in Drosophila","volume":"10","author":"Parra","year":"2000","journal-title":"Genome Res."},{"key":"2023012408503367800_b11","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1093\/nar\/12.1Part2.505","article-title":"Computer methods to locate signals in nucleic acid sequences","volume":"12","author":"Staden","year":"1984","journal-title":"Nucleic Acids Res."},{"key":"2023012408503367800_b12","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/0076-6879(90)83015-2","article-title":"Consensus patterns in DNA sequences","volume":"183","author":"Stormo","year":"1990","journal-title":"Meth. Enzymol."},{"key":"2023012408503367800_b13","volume-title":"The Gene Identification Problem from a Hypotheses Test Perspective","author":"Vilardell","year":"2004"},{"key":"2023012408503367800_b14","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1093\/hmg\/7.5.919","article-title":"Statistical features of human exons and their flanking regions","volume":"7","author":"Zhang","year":"1998","journal-title":"Hum. Mol. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/24\/3003\/48839092\/bioinformatics_22_24_3003.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/24\/3003\/48839092\/bioinformatics_22_24_3003.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:19:30Z","timestamp":1674551970000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/24\/3003\/209970"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,5,18]]},"references-count":14,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2006,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl544","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,12,15]]},"published":{"date-parts":[[2006,5,18]]}}}