{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:14:37Z","timestamp":1773274477443,"version":"3.50.1"},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"S6","license":[{"start":{"date-parts":[[2012,4,19]],"date-time":"2012-04-19T00:00:00Z","timestamp":1334793600000},"content-version":"tdm","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"],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>In this paper, we address the problem of identifying and quantifying polymorphisms in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the fundamental idea that each polymorphism corresponds to a recognisable pattern in a De Bruijn graph constructed from the RNA-seq reads, we propose a general model for all polymorphisms in such graphs. We then introduce an exact algorithm, called K<jats:sc>IS<\/jats:sc> S<jats:sc>PLICE<\/jats:sc>, to extract alternative splicing events.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We show that K<jats:sc>IS<\/jats:sc> S<jats:sc>PLICE<\/jats:sc> enables to identify more correct events than general purpose transcriptome assemblers. Additionally, on a 71 M reads dataset from human brain and liver tissues, K<jats:sc>IS<\/jats:sc> S<jats:sc>PLICE<\/jats:sc> identified 3497 alternative splicing events, out of which 56% are not present in the annotations, which confirms recent estimates showing that the complexity of alternative splicing has been largely underestimated so far.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We propose new models and algorithms for the detection of polymorphism in RNA-seq data. This opens the way to a new kind of studies on large HTS RNA-seq datasets, where the focus is not the global reconstruction of full-length transcripts, but local assembly of polymorphic regions. K<jats:sc>IS<\/jats:sc> S<jats:sc>PLICE<\/jats:sc> is available for download at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/alcovna.genouest.org\/kissplice\/\" ext-link-type=\"uri\">http:\/\/alcovna.genouest.org\/kissplice\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-s6-s5","type":"journal-article","created":{"date-parts":[[2019,12,11]],"date-time":"2019-12-11T01:59:07Z","timestamp":1576029547000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":80,"title":["KIS SPLICE: de-novo calling alternative splicing events from RNA-seq data"],"prefix":"10.1186","volume":"13","author":[{"given":"Gustavo AT","family":"Sacomoto","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janice","family":"Kielbassa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rayan","family":"Chikhi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raluca","family":"Uricaru","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pavlos","family":"Antoniou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-France","family":"Sagot","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Peterlongo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent","family":"Lacroix","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,4,19]]},"reference":[{"issue":"7221","key":"5142_CR1","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1038\/nature07509","volume":"456","author":"ET Wang","year":"2008","unstructured":"Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB: Alternative isoform regulation in human tissue transcriptomes. 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