Annotating genomes with massive-scale RNA sequencing

Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). Mainly because of the difficulty of aligning short reads on exon-exon junctions, no attempts have been made so far to use RNA-Seq for building gene models de novo, that is, in the absence of a set of known genes a...

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Autores principales: Denoeud, France, Aury, Jean-Marc, Da Silva, Corinne, Noel, Benjamin, Rogier, Odile, Delledonne, Massimo, Morgante, Michele, Valle, Giorgio, Wincker, Patrick, Scarpelli, Claude, Jaillon, Olivier, Artiguenave, François
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646279/
https://www.ncbi.nlm.nih.gov/pubmed/19087247
http://dx.doi.org/10.1186/gb-2008-9-12-r175
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author Denoeud, France
Aury, Jean-Marc
Da Silva, Corinne
Noel, Benjamin
Rogier, Odile
Delledonne, Massimo
Morgante, Michele
Valle, Giorgio
Wincker, Patrick
Scarpelli, Claude
Jaillon, Olivier
Artiguenave, François
author_facet Denoeud, France
Aury, Jean-Marc
Da Silva, Corinne
Noel, Benjamin
Rogier, Odile
Delledonne, Massimo
Morgante, Michele
Valle, Giorgio
Wincker, Patrick
Scarpelli, Claude
Jaillon, Olivier
Artiguenave, François
author_sort Denoeud, France
collection PubMed
description Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). Mainly because of the difficulty of aligning short reads on exon-exon junctions, no attempts have been made so far to use RNA-Seq for building gene models de novo, that is, in the absence of a set of known genes and/or splicing events. We present G-Mo.R-Se (Gene Modelling using RNA-Seq), an approach aimed at building gene models directly from RNA-Seq and demonstrate its utility on the grapevine genome.
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spelling pubmed-26462792009-02-23 Annotating genomes with massive-scale RNA sequencing Denoeud, France Aury, Jean-Marc Da Silva, Corinne Noel, Benjamin Rogier, Odile Delledonne, Massimo Morgante, Michele Valle, Giorgio Wincker, Patrick Scarpelli, Claude Jaillon, Olivier Artiguenave, François Genome Biol Method Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). Mainly because of the difficulty of aligning short reads on exon-exon junctions, no attempts have been made so far to use RNA-Seq for building gene models de novo, that is, in the absence of a set of known genes and/or splicing events. We present G-Mo.R-Se (Gene Modelling using RNA-Seq), an approach aimed at building gene models directly from RNA-Seq and demonstrate its utility on the grapevine genome. BioMed Central 2008 2008-12-16 /pmc/articles/PMC2646279/ /pubmed/19087247 http://dx.doi.org/10.1186/gb-2008-9-12-r175 Text en Copyright © 2008 Denoeud et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Denoeud, France
Aury, Jean-Marc
Da Silva, Corinne
Noel, Benjamin
Rogier, Odile
Delledonne, Massimo
Morgante, Michele
Valle, Giorgio
Wincker, Patrick
Scarpelli, Claude
Jaillon, Olivier
Artiguenave, François
Annotating genomes with massive-scale RNA sequencing
title Annotating genomes with massive-scale RNA sequencing
title_full Annotating genomes with massive-scale RNA sequencing
title_fullStr Annotating genomes with massive-scale RNA sequencing
title_full_unstemmed Annotating genomes with massive-scale RNA sequencing
title_short Annotating genomes with massive-scale RNA sequencing
title_sort annotating genomes with massive-scale rna sequencing
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646279/
https://www.ncbi.nlm.nih.gov/pubmed/19087247
http://dx.doi.org/10.1186/gb-2008-9-12-r175
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