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A Combinatorial Approach to Automatic Discovery of Cluster-Patterns

  • Revital Eres
  • Gad M. Landau
  • Laxmi Parida
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2812)

Abstract

Functionally related genes often appear in each others neighborhood on the genome, however the order of the genes may not be the same. These groups or clusters of genes may have an ancient evolutionary origin or may signify some other critical phenomenon and may also aid in function prediction of genes. Such gene clusters also aid toward solving the problem of local alignment of genes. Similarly, clusters of protein domains, albeit appearing in different orders in the protein sequence, suggest common functionality in spite of being nonhomologous. In the paper we address the problem of automatically discovering clusters of entities be it genes or domains: we formalize the abstract problem as a discovery problem called the πpattern problem and give an algorithm that automatically discovers the clusters of patterns in multiple data sequences. We take a model-less approach and introduce a notation for maximal patterns that drastically reduces the number of valid cluster patterns, without any loss of information, We demonstrate the automatic pattern discovery tool on motifs on E Coli protein sequences.

Keywords

Design and analysis of algorithms combinatorial algorithms on words discovery data mining clusters patterns motifs 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Revital Eres
    • 1
  • Gad M. Landau
    • 1
    • 2
  • Laxmi Parida
    • 3
  1. 1.Department of Computer ScienceHaifa UniversityHaifaIsrael
  2. 2.Department of Computer and Information SciencePolytechnic UniversityBrooklynUSA
  3. 3.Computational Biology CenterIBM TJ Watson Research CenterNew YorkUSA

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