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Authors: Petr Procházka ; Ondřej Cvacho ; Luboš Krčál and Jan Holub

Affiliation: Dep. of Theoretical Computer Science, Faculty of Information Technology, Czech Technical University in Prague, Thákurova 2700/9, Prague 6, Czech Republic

Keyword(s): Elastic Degenerate Strings, Genomic Sequences, Degenerate Pattern Matching, Pan-Genomics.

Abstract: Recently, the concept of Elastic Degenerate Strings (EDS) was introduced as a way of representing a sequenced population of the same species. Several on-line Elastic Degenerate String Matching (EDSM) algorithms were presented so far. Some of them provide practical implementation. We propose a new on-line EDSM algorithm BNDM-EDS. Our algorithm combines two traditional algorithms BNDM and the Shift-And that were adapted to the specifics needed by Elastic Degenerate Strings. BNDM-EDS is running in O(Nmdm w e) worst-case time. This implies O(Nm) time for small patterns, where m is the length of the searched pattern, N is the size of EDS, and w is the size of the computer word. The algorithm uses O(N + n) space, where n is the length of EDS. BNDM-EDS requires a simple preprocessing step with time and space O(m). Experimental results on real genomic data show superiority of BNDM-EDS over state-of-the-art algorithms.

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Paper citation in several formats:
Procházka, P.; Cvacho, O.; Krčál, L. and Holub, J. (2021). Backward Pattern Matching on Elastic Degenerate Strings. In Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - BIOINFORMATICS; ISBN 978-989-758-490-9; ISSN 2184-4305, SciTePress, pages 50-59. DOI: 10.5220/0010243600002865

@conference{bioinformatics21,
author={Petr Procházka. and Ond\v{r}ej Cvacho. and Luboš Krčál. and Jan Holub.},
title={Backward Pattern Matching on Elastic Degenerate Strings},
booktitle={Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - BIOINFORMATICS},
year={2021},
pages={50-59},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0010243600002865},
isbn={978-989-758-490-9},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - BIOINFORMATICS
TI - Backward Pattern Matching on Elastic Degenerate Strings
SN - 978-989-758-490-9
IS - 2184-4305
AU - Procházka, P.
AU - Cvacho, O.
AU - Krčál, L.
AU - Holub, J.
PY - 2021
SP - 50
EP - 59
DO - 10.5220/0010243600002865
PB - SciTePress

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