PMSGA: A FAST DNA FRAGMENT ASSEMBLER

Juho Mäkinen; Jorma Tarhio; Sami Khuri

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Paper

PMSGA: A FAST DNA FRAGMENT ASSEMBLER

Topics: Algorithms and Software Tools; Sequence Analysis

In Proceedings of the First International Conference on Bioinformatics - Volume 0BIOSTEC, 77-82, 2010 , Valencia, Spain

Authors: Juho Mäkinen ¹ ; Jorma Tarhio ¹ and Sami Khuri ²

Affiliations: ¹ Helsinki University of Technology, Finland ; ² San José State University, United States

Keyword(s): DNA sequencing, Fragment assembly, Pattern matching, Sequence reconstruction, String graph.

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

Abstract: The DNA fragment assembly is an essential step in DNA sequencing projects. Since DNA sequencers output fragments, the original genome must be reconstructed from these small reads. In this paper, a new fragment assembly algorithm, Pattern Matching based String Graph Assembler (PMSGA), is presented. The algorithm uses multipattern matching to detect overlaps and a minimum cost flow algorithm to detect repeats. Special care was taken to reduce the algorithm's run time without compromising the quality of the assembly. PMSGA was compared with well-known fragment assemblers. The algorithm is faster than other assemblers. PMSGA produced high quality assemblies with prokaryotic data sets. The results for eukaryotic data are comparable with other assemblers.

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Paper citation in several formats:

Mäkinen, J.; Tarhio, J. and Khuri, S. (2010). PMSGA: A FAST DNA FRAGMENT ASSEMBLER. In Proceedings of the First International Conference on Bioinformatics (BIOSTEC 2010) - BIOINFORMATICS; ISBN 978-989-674-019-1; ISSN 2184-4305, SciTePress, pages 77-82. DOI: 10.5220/0002580800770082

@conference{bioinformatics10,
author={Juho Mäkinen. and Jorma Tarhio. and Sami Khuri.},
title={PMSGA: A FAST DNA FRAGMENT ASSEMBLER},
booktitle={Proceedings of the First International Conference on Bioinformatics (BIOSTEC 2010) - BIOINFORMATICS},
year={2010},
pages={77-82},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002580800770082},
isbn={978-989-674-019-1},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the First International Conference on Bioinformatics (BIOSTEC 2010) - BIOINFORMATICS
TI - PMSGA: A FAST DNA FRAGMENT ASSEMBLER
SN - 978-989-674-019-1
IS - 2184-4305
AU - Mäkinen, J.
AU - Tarhio, J.
AU - Khuri, S.
PY - 2010
SP - 77
EP - 82
DO - 10.5220/0002580800770082
PB - SciTePress