Vectorized Character Counting for Faster Pattern Matching

Roman Snytsar

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Paper

Vectorized Character Counting for Faster Pattern Matching

Topics: Algorithms and Software Tools; Next Generation Sequencing

In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOSTEC, 149-154, 2019 , Prague, Czech Republic

Author: Roman Snytsar

Affiliation: Microsoft Research, One Microsoft Way, Redmond WA 98052, U.S.A.

Keyword(s): Parallel Processing, Vectorization, Bioinformatics, FM-Index.

Abstract: Many modern sequence alignment tools implement fast string matching using the space efficient data structure called a FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper, we explore the opportunities for parallelization of the exact and inexact matches, and present an efficient solution for the Occ portion of the algorithm that utilizes the instruction-level parallelism of the modern CPUs. Our implementation computes all eight Occ values required for the inexact match algorithm step in a single pass. We showcase the algorithm performance in a multi-core genome aligner and discuss effects of the memory prefetch.

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Paper citation in several formats:

Snytsar, R. (2019). Vectorized Character Counting for Faster Pattern Matching. In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - BIOINFORMATICS; ISBN 978-989-758-353-7; ISSN 2184-4305, SciTePress, pages 149-154. DOI: 10.5220/0007258201490154

@conference{bioinformatics19,
author={Roman Snytsar.},
title={Vectorized Character Counting for Faster Pattern Matching},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - BIOINFORMATICS},
year={2019},
pages={149-154},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007258201490154},
isbn={978-989-758-353-7},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - BIOINFORMATICS
TI - Vectorized Character Counting for Faster Pattern Matching
SN - 978-989-758-353-7
IS - 2184-4305
AU - Snytsar, R.
PY - 2019
SP - 149
EP - 154
DO - 10.5220/0007258201490154
PB - SciTePress