On-line Searching in IUPAC Nucleotide Sequences

Petr Procházka, Jan Holub

2019

Abstract

We propose a novel pattern matching algorithm for consensus nucleotide sequences over IUPAC alphabet, called BADPM (Byte-Aligned Degenerate Pattern Matching). The consensus nucleotide sequences represent a consensus obtained by sequencing a population of the same species and they are considered as so-called degenerate strings. BADPM works at the level of single bytes and it achieves sublinear search time on average. The algorithm is based on tabulating all possible factors of the searched pattern. It needs O(m + mα2 logm)space data structure and O(mα2) time for preprocessing where m is a length of the pattern and α represents a maximum number of variants implied from a 4-gram over IUPAC alphabet. The worst-case locate time is bounded by O(nm2α4) for BADPM where n is the length of the input text. However, the experiments performed on real genomic data proved the sublinear search time. BADPM can easily cooperate with the block q-gram inverted index and so achieve still better locate time. We implemented two other pattern matching algorithms for IUPAC nucleotide sequences as a baseline: Boyer-Moore-Horspool (BMH) and Parallel Naive Search (PNS). Especially PNS proves its efficiency insensitive to the length of the searched pattern m. BADPM proved its strong superiority for searching middle and long patterns.

Paper Citation

in Harvard Style

Procházka P. and Holub J. (2019). On-line Searching in IUPAC Nucleotide Sequences. 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 66-77. DOI: 10.5220/0007382900660077

in Bibtex Style

@conference{bioinformatics19,
author={Petr Procházka and Jan Holub},
title={On-line Searching in IUPAC Nucleotide Sequences},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019) - Volume 3: BIOINFORMATICS},
year={2019},
pages={66-77},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007382900660077},
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 - On-line Searching in IUPAC Nucleotide Sequences
SN - 978-989-758-353-7
AU - Procházka P.
AU - Holub J.
PY - 2019
SP - 66
EP - 77
DO - 10.5220/0007382900660077
PB - SciTePress