{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T11:08:00Z","timestamp":1761217680701},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput sequencing of RNA in vivo facilitates many applications, not the least of which is the cataloging of variant splice isoforms of protein-coding messenger RNAs. Although many solutions have been proposed for reconstructing putative isoforms from deep sequencing data, these generally take as their substrate the collective alignment structure of RNA-seq reads and ignore the biological signals present in the actual nucleotide sequence. The majority of these solutions are graph-theoretic, relying on a splice graph representing the splicing patterns and exon expression levels indicated by the spliced-alignment process.<\/jats:p>\n               <jats:p>Results: We show how to augment splice graphs with additional information reflecting the biology of transcription, splicing and translation, to produce what we call an ORF (open reading frame) graph . We then show how ORF graphs can be used to produce isoform predictions with higher accuracy than current state-of-the-art approaches.<\/jats:p>\n               <jats:p>Availability and implementation : RSVP is available as C++ source code under an open-source licence: http:\/\/ohlerlab.mdc-berlin.de\/software\/RSVP\/ .<\/jats:p>\n               <jats:p>Contact: \u00a0bmajoros@duke.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu160","type":"journal-article","created":{"date-parts":[[2014,3,23]],"date-time":"2014-03-23T00:40:14Z","timestamp":1395535214000},"page":"1958-1964","source":"Crossref","is-referenced-by-count":5,"title":["Improved transcript isoform discovery using ORF graphs"],"prefix":"10.1093","volume":"30","author":[{"given":"William H.","family":"Majoros","sequence":"first","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA, 2 Institute for Genome Sciences and Policy, Duke University, Durham, NC 27705, USA, 3 Department of Computer Science, Duke University, Durham, NC 27708, USA, 4 Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA, 5 Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin 13125, Germany and 6 Department of Biology, Humboldt University of Berlin, Berlin 10115, Germany"},{"name":"1 Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA, 2 Institute for Genome Sciences and Policy, Duke University, Durham, NC 27705, USA, 3 Department of Computer Science, Duke University, Durham, NC 27708, USA, 4 Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA, 5 Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin 13125, Germany and 6 Department of Biology, Humboldt University of Berlin, Berlin 10115, Germany"}]},{"given":"Niel","family":"Lebeck","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA, 2 Institute for Genome Sciences and Policy, Duke University, Durham, NC 27705, USA, 3 Department of Computer Science, Duke University, Durham, NC 27708, USA, 4 Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA, 5 Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin 13125, Germany and 6 Department of Biology, Humboldt University of Berlin, Berlin 10115, Germany"}]},{"given":"Uwe","family":"Ohler","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA, 2 Institute for Genome Sciences and Policy, Duke University, Durham, NC 27705, USA, 3 Department of Computer Science, Duke University, Durham, NC 27708, USA, 4 Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA, 5 Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin 13125, Germany and 6 Department of Biology, Humboldt University of Berlin, Berlin 10115, Germany"},{"name":"1 Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA, 2 Institute for Genome Sciences and Policy, Duke University, Durham, NC 27705, USA, 3 Department of Computer Science, Duke University, Durham, NC 27708, USA, 4 Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA, 5 Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin 13125, Germany and 6 Department of Biology, Humboldt University of Berlin, Berlin 10115, Germany"},{"name":"1 Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA, 2 Institute for Genome Sciences and Policy, Duke University, Durham, NC 27705, USA, 3 Department of Computer Science, Duke University, Durham, NC 27708, USA, 4 Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA, 5 Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin 13125, Germany and 6 Department of Biology, Humboldt University of Berlin, Berlin 10115, Germany"},{"name":"1 Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA, 2 Institute for Genome Sciences and Policy, Duke University, Durham, NC 27705, USA, 3 Department of Computer Science, Duke University, Durham, NC 27708, USA, 4 Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA, 5 Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin 13125, Germany and 6 Department of Biology, Humboldt University of Berlin, Berlin 10115, Germany"}]},{"given":"Song","family":"Li","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA, 2 Institute for Genome Sciences and Policy, Duke University, Durham, NC 27705, USA, 3 Department of Computer Science, Duke University, Durham, NC 27708, USA, 4 Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA, 5 Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin 13125, Germany and 6 Department of Biology, Humboldt University of Berlin, Berlin 10115, Germany"}]}],"member":"286","published-online":{"date-parts":[[2014,3,22]]},"reference":[{"key":"2023012711241337800_btu160-B1","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2006-7-s1-s9","article-title":"JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions","volume":"7","author":"Allen","year":"2006","journal-title":"Genome 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