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We present an algorithm for reference annotation-based transcript assembly and show how it can be used to rapidly investigate novel transcripts revealed by RNA-Seq in comparison with a reference annotation.<\/jats:p>\n               <jats:p>Availability: The methods described in this article are implemented in the Cufflinks suite of software for RNA-Seq, freely available from http:\/\/bio.math.berkeley.edu\/cufflinks. The software is released under the BOOST license.<\/jats:p>\n               <jats:p>Contact: \u00a0cole@broadinstitute.org; lpachter@math.berkeley.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr355","type":"journal-article","created":{"date-parts":[[2011,6,23]],"date-time":"2011-06-23T00:58:29Z","timestamp":1308790709000},"page":"2325-2329","source":"Crossref","is-referenced-by-count":853,"title":["Identification of novel transcripts in annotated genomes using RNA-Seq"],"prefix":"10.1093","volume":"27","author":[{"given":"Adam","family":"Roberts","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, UC Berkeley, Berkeley, CA, 2Department of Stem Cell and Regenerative Biology, Harvard University and The Broad Institute of MIT and Harvard, 3Department of Mathematics and 4Department of and Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA"}]},{"given":"Harold","family":"Pimentel","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, UC Berkeley, Berkeley, CA, 2Department of Stem Cell and Regenerative Biology, Harvard University and The Broad Institute of MIT and Harvard, 3Department of Mathematics and 4Department of and Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA"}]},{"given":"Cole","family":"Trapnell","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, UC Berkeley, Berkeley, CA, 2Department of Stem Cell and Regenerative Biology, Harvard University and The Broad Institute of MIT and Harvard, 3Department of Mathematics and 4Department of and Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA"}]},{"given":"Lior","family":"Pachter","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, UC Berkeley, Berkeley, CA, 2Department of Stem Cell and Regenerative Biology, Harvard University and The Broad Institute of MIT and Harvard, 3Department of Mathematics and 4Department of and Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA"},{"name":"1 Department of Computer Science, UC Berkeley, Berkeley, CA, 2Department of Stem Cell and Regenerative Biology, Harvard University and The Broad Institute of MIT and Harvard, 3Department of Mathematics and 4Department of and Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA"},{"name":"1 Department of Computer Science, UC Berkeley, Berkeley, CA, 2Department of Stem Cell and Regenerative Biology, Harvard University and The Broad Institute of MIT and Harvard, 3Department of Mathematics and 4Department of and Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,6,21]]},"reference":[{"key":"2023012511524862500_B1","doi-asserted-by":"crossref","first-page":"1651","DOI":"10.1126\/science.2047873","article-title":"Complementary DNA sequencing: expressed sequence tags and human genome project","volume":"252","author":"Adams","year":"1991","journal-title":"Science"},{"key":"2023012511524862500_B2","doi-asserted-by":"crossref","first-page":"3596","DOI":"10.1093\/bioinformatics\/bti609","article-title":"JIGSAW: integration of multiple sources of evidence for gene prediction","volume":"21","author":"Allen","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012511524862500_B3","doi-asserted-by":"crossref","first-page":"D459","DOI":"10.1093\/nar\/gki135","article-title":"The Vertebrate Genome Annotation (VEGA) database","volume":"33","author":"Ashurst","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012511524862500_B4","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/458239a","article-title":"Transcriptomics: the digital generation","volume":"458","author":"Blow","year":"2009","journal-title":"Nature"},{"key":"2023012511524862500_B5","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btp459","article-title":"Rna-mate: a recursive mapping strategy for high-throughput rna-sequencing data","author":"Cloonan","year":"2009","journal-title":"Bioinformatics."},{"key":"2023012511524862500_B6","doi-asserted-by":"crossref","first-page":"R175","DOI":"10.1186\/gb-2008-9-12-r175","article-title":"Annotating genomes with massive-scale RNA-sequencing","volume":"9","author":"Denoued","year":"2008","journal-title":"Genome Biol."},{"key":"2023012511524862500_B7","doi-asserted-by":"crossref","first-page":"e1000074","DOI":"10.1371\/journal.pcbi.1000074","article-title":"Viral population estimation using pyrosequencing","volume":"4","author":"Eriksson","year":"2008","journal-title":"PLoS Comput. 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