{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T06:18:22Z","timestamp":1762323502225},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: It was previously demonstrated that splicing elements are positional dependent. We exploited this relationship between location and function by comparing positional distributions between all possible 4096 hexamers around a database of human splice sites. The distance measure used in this study found point mutations that produced higher distances disrupted splicing, whereas point mutations with smaller distances generally had no effect on splicing. Reasoning the idea that functional splicing elements have signature positional distributions around constitutively spliced exons, we introduce Spliceman\u2014an online tool that predicts how likely distant mutations around annotated splice sites were to disrupt splicing. Spliceman takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation included the analyses of 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish.<\/jats:p>\n               <jats:p>Availability: Freely available on the web at http:\/\/fairbrother.biomed.brown.edu\/spliceman\/<\/jats:p>\n               <jats:p>Contact: \u00a0fairbrother@brown.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts074","type":"journal-article","created":{"date-parts":[[2012,2,11]],"date-time":"2012-02-11T04:47:14Z","timestamp":1328935634000},"page":"1031-1032","source":"Crossref","is-referenced-by-count":50,"title":["Spliceman\u2014a computational web server that predicts sequence variations in pre-mRNA splicing"],"prefix":"10.1093","volume":"28","author":[{"given":"Kian Huat","family":"Lim","sequence":"first","affiliation":[{"name":"1 Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02903 and 2Center of Computational Molecular Biology, Brown University, Providence, RI 02012, USA"}]},{"given":"William Guy","family":"Fairbrother","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02903 and 2Center of Computational Molecular Biology, Brown University, Providence, RI 02012, USA"},{"name":"1 Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI 02903 and 2Center of Computational Molecular Biology, Brown University, Providence, RI 02012, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,2,10]]},"reference":[{"key":"2023012512215996600_B1","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1126\/science.1073774","article-title":"Predictive identification of exonic splicing enhancers in human genes","volume":"297","author":"Fairbrother","year":"2002","journal-title":"Science"},{"key":"2023012512215996600_B2","doi-asserted-by":"crossref","first-page":"D493","DOI":"10.1093\/nar\/gkh103","article-title":"The UCSC Table Browser data retrieval tool","volume":"1","author":"Karolchik","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012512215996600_B3","doi-asserted-by":"crossref","first-page":"11093","DOI":"10.1073\/pnas.1101135108","article-title":"Using positional distribution to identify splicing elements and predict mRNA processing defects in human genes","volume":"108","author":"Lim","year":"2011","journal-title":"Proc. Acad. Sci. USA"},{"key":"2023012512215996600_B4","doi-asserted-by":"crossref","first-page":"1900","DOI":"10.1016\/j.febslet.2005.02.047","article-title":"Are splicing mutations most frequent cause of hereditary disease?","volume":"579","author":"Lopez-Bigas","year":"2005","journal-title":"FEBS Lett."},{"key":"2023012512215996600_B5","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1101\/gr.361602","article-title":"The Bioperl toolkit: Perl modules for the life sciences","volume":"12","author":"Stajicn","year":"2002","journal-title":"Genome Res."},{"key":"2023012512215996600_B6","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1002\/humu.10212","article-title":"Human Gene Mutation Database (HGMD): 2003 update","volume":"21","author":"Stenson","year":"2003","journal-title":"Hum. Mutat."},{"key":"2023012512215996600_B7","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1101\/gad.1195304","article-title":"Computational definition of sequence motifs governing constitutive exon splicing","volume":"11","author":"Zhang","year":"2004","journal-title":"Genes Dev."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/7\/1031\/48878878\/bioinformatics_28_7_1031.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/7\/1031\/48878878\/bioinformatics_28_7_1031.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:47:44Z","timestamp":1674661664000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/7\/1031\/210474"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,2,10]]},"references-count":7,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2012,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts074","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,4,1]]},"published":{"date-parts":[[2012,2,10]]}}}