{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:29:02Z","timestamp":1767961742418,"version":"3.49.0"},"reference-count":64,"publisher":"Springer Science and Business Media LLC","issue":"S10","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>For splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to solve these tasks.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this work we consider Support Vector Machines for splice site recognition. We employ the so-called <jats:italic>weighted degree<\/jats:italic> kernel which turns out well suited for this task, as we will illustrate in several experiments where we compare its prediction accuracy with that of recently proposed systems. We apply our method to the <jats:italic>genome-wide<\/jats:italic> recognition of splice sites in <jats:italic>Caenorhabditis elegans<\/jats:italic>, <jats:italic>Drosophila melanogaster<\/jats:italic>, <jats:italic>Arabidopsis thaliana<\/jats:italic>, <jats:italic>Danio rerio<\/jats:italic>, and <jats:italic>Homo sapiens<\/jats:italic>. Our performance estimates indicate that splice sites can be recognized very accurately in these genomes and that our method outperforms many other methods including <jats:italic>Markov Chains<\/jats:italic>, <jats:italic>GeneSplicer<\/jats:italic> and <jats:italic>SpliceMachine<\/jats:italic>. We provide genome-wide predictions of splice sites and a stand-alone prediction tool ready to be used for incorporation in a gene finder.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Availability<\/jats:title>\n            <jats:p>Data, splits, additional information on the model selection, the whole genome predictions, as well as the stand-alone prediction tool are available for download at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.fml.mpg.de\/raetsch\/projects\/splice\" ext-link-type=\"uri\">http:\/\/www.fml.mpg.de\/raetsch\/projects\/splice<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-8-s10-s7","type":"journal-article","created":{"date-parts":[[2007,12,21]],"date-time":"2007-12-21T19:14:01Z","timestamp":1198264441000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":119,"title":["Accurate splice site prediction using support vector machines"],"prefix":"10.1186","volume":"8","author":[{"given":"S\u00f6ren","family":"Sonnenburg","sequence":"first","affiliation":[]},{"given":"Gabriele","family":"Schweikert","sequence":"additional","affiliation":[]},{"given":"Petra","family":"Philips","sequence":"additional","affiliation":[]},{"given":"Jonas","family":"Behr","sequence":"additional","affiliation":[]},{"given":"Gunnar","family":"R\u00e4tsch","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2007,12,21]]},"reference":[{"issue":"Suppl 1","key":"1984_CR1","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1186\/gb-2006-7-s1-s3","volume":"7","author":"V Bajic","year":"2006","unstructured":"Bajic V, Brent M, Brown R, Frankish A, Harrow J, Ohler U, Solovyev V, Tan S: Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. 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