LINEAR--TIME MATCHING OF POSITION WEIGHT MATRICES

Nikola Stojanovic

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Paper

LINEAR--TIME MATCHING OF POSITION WEIGHT MATRICES

Topics: Algorithms and Software Tools; Genomics and Proteomics; Sequence Analysis

In Proceedings of the First International Conference on Bioinformatics - Volume 0BIOSTEC, 66-73, 2010 , Valencia, Spain

Author: Nikola Stojanovic

Affiliation: University of Texas at Arlington, United States

Keyword(s): DNA motifs, Position weight matrices, Genome–wide analysis, Algorithms, Genomics, Pattern matching.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Sequence Analysis

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.

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Paper citation in several formats:

Stojanovic, N. (2010). LINEAR--TIME MATCHING OF POSITION WEIGHT MATRICES. In Proceedings of the First International Conference on Bioinformatics (BIOSTEC 2010) - BIOINFORMATICS; ISBN 978-989-674-019-1; ISSN 2184-4305, SciTePress, pages 66-73. DOI: 10.5220/0002750500660073

@conference{bioinformatics10,
author={Nikola Stojanovic.},
title={LINEAR--TIME MATCHING OF POSITION WEIGHT MATRICES},
booktitle={Proceedings of the First International Conference on Bioinformatics (BIOSTEC 2010) - BIOINFORMATICS},
year={2010},
pages={66-73},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002750500660073},
isbn={978-989-674-019-1},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the First International Conference on Bioinformatics (BIOSTEC 2010) - BIOINFORMATICS
TI - LINEAR--TIME MATCHING OF POSITION WEIGHT MATRICES
SN - 978-989-674-019-1
IS - 2184-4305
AU - Stojanovic, N.
PY - 2010
SP - 66
EP - 73
DO - 10.5220/0002750500660073
PB - SciTePress