LINEAR--TIME MATCHING OF POSITION WEIGHT MATRICES

Nikola Stojanovic

2010

Abstract

Position Weight Matrices are a popular way of representing variable motifs in genomic sequences, and they have been widely used for describing the binding sites of transcriptional proteins. However, the standard implementation of PWM matching, while not inefficient on shorter sequences, is too expensive for whole– genome searches. In this paper we present an algorithm we have developed for efficient matching of PWMs in long target sequences. After the initial pre–processing of the matrix it performs in time linear to the size of the genomic segment.

Paper Citation

in Harvard Style

Stojanovic N. (2010). LINEAR--TIME MATCHING OF POSITION WEIGHT MATRICES . In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 66-73. DOI: 10.5220/0002750500660073

in Bibtex Style

@conference{bioinformatics10,
author={Nikola Stojanovic},
title={LINEAR--TIME MATCHING OF POSITION WEIGHT MATRICES},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={66-73},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002750500660073},
isbn={978-989-674-019-1},
}

in EndNote Style

TY - CONF
JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - LINEAR--TIME MATCHING OF POSITION WEIGHT MATRICES
SN - 978-989-674-019-1
AU - Stojanovic N.
PY - 2010
SP - 66
EP - 73
DO - 10.5220/0002750500660073