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Authors: Michaël Vyverman 1 ; Dieter De Smedt 1 ; Yao-Cheng Lin 2 ; Lieven Sterck 2 ; Bernard De Baets 1 ; Veerle Fack 1 and Peter Dawyndt 1

Affiliations: 1 Ghent University, Belgium ; 2 VIB and Ghent University, Belgium

ISBN: 978-989-758-012-3

Keyword(s): Spliced Alignment, Splice Site Detection, Read Mapping, Long Reads, cDNA Mapping, RNA-seq.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Next Generation Sequencing ; Sequence Analysis ; Transcriptomics

Abstract: Mapping and alignment of cDNA sequences containing splice sites is an algorithmically and computationally challenging task. Most recently developed spliced aligners are designed for mapping short reads and sacrifice sensitivity for increased performance. We present mesalina, a highly accurate spliced aligner, that can also be used to detect novel non-canonical splice sites and whose performance is more robust with respect to increasing read length. Mesalina utilizes the seed-extend strategy, combining fast retrieval of maximal exact matches with a sensitive sandwich dynamic programming algorithm. Preliminary results indicate that mesalina is accurate and very fast, especially for mapping longer reads. In particular, it is more than ten times faster than mappers with a comparable accuracy. Mesalina is available from https://github.ugent.be/ComputationalBiology/mesalina.

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Paper citation in several formats:
Vyverman, M.; De Smedt, D.; Lin, Y.; Sterck, L.; De Baets, B.; Fack, V. and Dawyndt, P. (2014). Fast and Accurate cDNA Mapping and Splice Site Identification.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014) ISBN 978-989-758-012-3, pages 233-238. DOI: 10.5220/0004903502330238

@conference{bioinformatics14,
author={Michaël Vyverman. and Dieter De Smedt. and Yao{-}Cheng Lin. and Lieven Sterck. and Bernard De Baets. and Veerle Fack. and Peter Dawyndt.},
title={Fast and Accurate cDNA Mapping and Splice Site Identification},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)},
year={2014},
pages={233-238},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004903502330238},
isbn={978-989-758-012-3},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)
TI - Fast and Accurate cDNA Mapping and Splice Site Identification
SN - 978-989-758-012-3
AU - Vyverman, M.
AU - De Smedt, D.
AU - Lin, Y.
AU - Sterck, L.
AU - De Baets, B.
AU - Fack, V.
AU - Dawyndt, P.
PY - 2014
SP - 233
EP - 238
DO - 10.5220/0004903502330238

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