HAL: hal-00784407, version 1

PubMed: 22537044

PubMed Central: 3358658

DOI: 10.1186/1471-2105-13-S6-S5

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BMC Bioinformatics 13, Suppl 6 (2012) S5

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data

Gustavo Sacomoto 1, 2, Janice Kielbassa 1, 2, Rayan Chikhi 3, Raluca Uricaru 1, 3, 4, Pavlos Antoniou 1, Marie-France Sagot 1, 2, Pierre Peterlongo (  Author to contact preferably ) 3, Vincent Lacroix (  Author to contact preferably ) 1, 2

(2012)

In this paper, we address the problem of identifying and quantifying polymorphisms in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the fundamental idea that each polymorphism corresponds to a recognisable pattern in a De Bruijn graph constructed from the RNA-seq reads, we propose a general model for all polymorphisms in such graphs. We then introduce an exact algorithm, called KISSPLICE, to extract alternative splicing events. We show that KISSPLICE enables to identify more correct events than general purpose transcriptome assemblers. Additionally, on a 71 M reads dataset from human brain and liver tissues, KISSPLICE identified 3497 alternative splicing events, out of which 56% are not present in the annotations, which confirms recent estimates showing that the complexity of alternative splicing has been largely underestimated so far. We propose new models and algorithms for the detection of polymorphism in RNA-seq data. This opens the way to a new kind of studies on large HTS RNA-seq datasets, where the focus is not the global reconstruction of full-length transcripts, but local assembly of polymorphic regions. KISSPLICE is available for download at http://alcovna.genouest.org/kissplice/.

1:	Laboratoire de Biométrie et Biologie Evolutive (LBBE)
	Université Claude Bernard - Lyon I – CNRS : UMR5558 – INRIA
2:	BAMBOO (LBBE Lyon / INRIA Grenoble Rhône-Alpes)
	Université Claude Bernard - Lyon I – INRIA – CNRS : UMR5558 – Laboratoire de Biométrie et Biologie Evolutive
3:	GENSCALE (INRIA - IRISA)
	INRIA – CNRS : UMR6074 – Université de Rennes 1 – École normale supérieure de Cachan - ENS Cachan
4:	Amélioration des Plantes et Biotechnologies Végétales (APBV)
	Institut national de la recherche agronomique (INRA) : UMR118 – Agrocampus Ouest – Université de Rennes 1

Domain

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Life Sciences/Biochemistry, Molecular Biology/Genomics Life Sciences/Quantitative Methods Computer Science/Bioinformatics

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Submitted on: Monday, 4 February 2013 13:01:21

Updated on: Friday, 8 February 2013 10:15:34