title: CIDANE: comprehensive isoform discovery and abundance estimation.
abstract: We present CIDANE, a novel framework for genome-based transcript reconstruction and quantification from RNA-seq reads. CIDANE assembles transcripts efficiently with significantly higher sensitivity and precision than existing tools. Its algorithmic core not only reconstructs transcripts ab initio, but also allows the use of the growing annotation of known splice sites, transcription start and end sites, or full-length transcripts, which are available for most model organisms. CIDANE supports the integrated analysis of RNA-seq and additional gene-boundary data and recovers splice junctions that are invisible to other methods. CIDANE is available at http://ccb.jhu.edu/software/cidane/.
authors.affiliation: Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.|Toyota Technological Institute at Chicago, 6045 S. Kennwood Avenue, Chicago, IL 60637, USA.
authors.forename: Stefan
authors.initials: S
authors.lastname: Canzar
authors.affiliation: Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany.
authors.forename: Sandro
authors.initials: S
authors.lastname: Andreotti
authors.affiliation: Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany. david.weese@fu-berlin.de.
authors.forename: David
authors.initials: D
authors.lastname: Weese
authors.affiliation: Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany. knut.reinert@fu-berlin.de.
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
authors.affiliation: Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, Amsterdam, 1098 XG, The Netherlands. gunnar.klau@cwi.nl.
authors.forename: Gunnar W
authors.initials: GW
authors.lastname: Klau
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020033:Protein Isoforms / Q000235:genetics* / Q000302:isolation & purification; D012313:RNA / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome / Q000235:genetics
chemical_list: D020033:Protein Isoforms; D012313:RNA
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