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Author: Jaime Seguel

Affiliation: University of Puerto Rico, United States

Keyword(s): Sequence Alignment, Parallel Computation, Recursion, Mapping Assembly.

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

Abstract: This paper focuses on mathematical definitions and results that prove the correctness of a parallel algorithm for mapping assembly. The mathematical concepts and facts discussed here establish the reach and limitations of a combination of Smith-Waterman local alignment method and Hirschberg’s divide-and-conquer longest common subsequence determination method. The parallel algorithm, whose correctness is proved, is a general method that works best for solving the problem of the local alignment of a short and a very large sequence, such as an entire genome. The method is thus, suitable for mapping assembly, where millions of short sequence segments, the so-called reads, are aligned with a whole genome.

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Paper citation in several formats:
Seguel, J. (2014). Mathematics of the Design of a Parallel Mapping Assembly Algorithm - Combining Smith-Waterman and Hirschberg’s LCS Methods. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2014) - BIOINFORMATICS; ISBN 978-989-758-012-3; ISSN 2184-4305, SciTePress, pages 221-226. DOI: 10.5220/0004883802210226

@conference{bioinformatics14,
author={Jaime Seguel.},
title={Mathematics of the Design of a Parallel Mapping Assembly Algorithm - Combining Smith-Waterman and Hirschberg’s LCS Methods},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2014) - BIOINFORMATICS},
year={2014},
pages={221-226},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004883802210226},
isbn={978-989-758-012-3},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2014) - BIOINFORMATICS
TI - Mathematics of the Design of a Parallel Mapping Assembly Algorithm - Combining Smith-Waterman and Hirschberg’s LCS Methods
SN - 978-989-758-012-3
IS - 2184-4305
AU - Seguel, J.
PY - 2014
SP - 221
EP - 226
DO - 10.5220/0004883802210226
PB - SciTePress

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