Latest Advances in Solving the All-Pairs Suffix Prefix Problem

Maan Haj Rachid

2019

Abstract

Finding the overlaps between sequences that are generated by Next Generation Sequencing (NGS) technology is a time- and space-consuming step in building a string graph in genome assembly. The problem is known in computer science as all-pairs suffix prefix (APSP). The problem has been tackled since 1992 and several solutions were presented to solve it. While some of them achieve optimal theoretical time consumption, they have a very high space-consumption in addition to being practically slow due to a raised constant factor. Some other recent solutions practically consume much less space and time to solve APSP despite their adaptations to techniques and data structures which don’t have optimal worst-case asymptotic complexity. Other few researches tackled the approximate version of the overlap problem hoping to avoid error-detecting stages in genome assembly. These solutions used the same data structures which were employed to solve APSP in addition to some advanced techniques in order to address the complexity of approximate matching. In this work, we evaluate these recent algorithms, in terms of time and space, in both exact and approximate formats. Our results show that FastAPSP has the best time-consumption unless the size of the data set is large. The high space demand of such large data sets would favor the usage of SOF and Readjoiner. Our experiments also show that AOF is, in general, faster than FM unless the data set is small and repetitive. In addition, it can handle large data sets that cannot be processed by FM.

Paper Citation

in Harvard Style

Rachid M. (2019). Latest Advances in Solving the All-Pairs Suffix Prefix Problem. In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-353-7, SciTePress, pages 174-181. DOI: 10.5220/0007369801740181

in Bibtex Style

@conference{bioinformatics19,
author={Maan Haj Rachid},
title={Latest Advances in Solving the All-Pairs Suffix Prefix Problem},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS},
year={2019},
pages={174-181},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007369801740181},
isbn={978-989-758-353-7},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS
TI - Latest Advances in Solving the All-Pairs Suffix Prefix Problem
SN - 978-989-758-353-7
AU - Rachid M.
PY - 2019
SP - 174
EP - 181
DO - 10.5220/0007369801740181
PB - SciTePress