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Authors: Michaël Vyverman ; Joachim De Schrijver ; Wim Van Criekinge ; Peter Dawyndt and Veerle Fack

Affiliation: Ghent University, Belgium

Keyword(s): Inexact string matching, DNA sequencing, Read mapping, Enhanced suffix arrays.

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

Abstract: With the rise of high throughput sequencing, new programs have been developed for dealing with the alignment of a huge amount of short read data to reference genomes. Recent developments in sequencing technology allow longer reads, but the mappers for short reads are not suited for reads of several hundreds of base pairs. We propose an algorithm for mapping longer reads, which is based on chaining maximal exact matches and uses heuristics and the Needleman-Wunsch algorithm to bridge the gaps. To compute maximal exact matches we use a specialized index structure, called enhanced suffix array. The proposed algorithm is very accurate and can handle large reads with mutations and long insertions and deletions.

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Paper citation in several formats:
Vyverman, M.; De Schrijver, J.; Van Criekinge, W.; Dawyndt, P. and Fack, V. (2011). ACCURATE LONG READ MAPPING USING ENHANCED SUFFIX ARRAYS. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS; ISBN 978-989-8425-36-2; ISSN 2184-4305, SciTePress, pages 102-107. DOI: 10.5220/0003126201020107

@conference{bioinformatics11,
author={Michaël Vyverman. and Joachim {De Schrijver}. and Wim {Van Criekinge}. and Peter Dawyndt. and Veerle Fack.},
title={ACCURATE LONG READ MAPPING USING ENHANCED SUFFIX ARRAYS},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS},
year={2011},
pages={102-107},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003126201020107},
isbn={978-989-8425-36-2},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2011) - BIOINFORMATICS
TI - ACCURATE LONG READ MAPPING USING ENHANCED SUFFIX ARRAYS
SN - 978-989-8425-36-2
IS - 2184-4305
AU - Vyverman, M.
AU - De Schrijver, J.
AU - Van Criekinge, W.
AU - Dawyndt, P.
AU - Fack, V.
PY - 2011
SP - 102
EP - 107
DO - 10.5220/0003126201020107
PB - SciTePress

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