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CIDANE: comprehensive isoform discovery and abundance estimation

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, b...

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Detalles Bibliográficos
Autores principales: Canzar, Stefan, Andreotti, Sandro, Weese, David, Reinert, Knut, Klau, Gunnar W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734886/
https://www.ncbi.nlm.nih.gov/pubmed/26831908
http://dx.doi.org/10.1186/s13059-015-0865-0
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author Canzar, Stefan
Andreotti, Sandro
Weese, David
Reinert, Knut
Klau, Gunnar W.
author_facet Canzar, Stefan
Andreotti, Sandro
Weese, David
Reinert, Knut
Klau, Gunnar W.
author_sort Canzar, Stefan
collection PubMed
description 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/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0865-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-47348862016-02-02 CIDANE: comprehensive isoform discovery and abundance estimation Canzar, Stefan Andreotti, Sandro Weese, David Reinert, Knut Klau, Gunnar W. Genome Biol Method 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/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0865-0) contains supplementary material, which is available to authorized users. BioMed Central 2016-01-30 2016 /pmc/articles/PMC4734886/ /pubmed/26831908 http://dx.doi.org/10.1186/s13059-015-0865-0 Text en © Canzar et al. 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Canzar, Stefan
Andreotti, Sandro
Weese, David
Reinert, Knut
Klau, Gunnar W.
CIDANE: comprehensive isoform discovery and abundance estimation
title CIDANE: comprehensive isoform discovery and abundance estimation
title_full CIDANE: comprehensive isoform discovery and abundance estimation
title_fullStr CIDANE: comprehensive isoform discovery and abundance estimation
title_full_unstemmed CIDANE: comprehensive isoform discovery and abundance estimation
title_short CIDANE: comprehensive isoform discovery and abundance estimation
title_sort cidane: comprehensive isoform discovery and abundance estimation
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734886/
https://www.ncbi.nlm.nih.gov/pubmed/26831908
http://dx.doi.org/10.1186/s13059-015-0865-0
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