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Efficient Searching for Motifs in DNA Sequences Using Position Weight Matrices

  • Nikola Stojanovic
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 127)

Abstract

Searching genomic sequences for motifs representing functionally important sites is a significant and well–established subfield of bioinformatics. In that context, Position Weight Matrices are a popular way of representing variable motifs, as 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.

Keywords

DNA motifs Position weight matrices Genome–wide analysis Algorithms Genomics Pattern matching 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Nikola Stojanovic
    • 1
  1. 1.Department of Computer Science and EngineeringUniversity of Texas at ArlingtonArlingtonU.S.A.

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