Motif Patterns in 2D

Simona Ester Rombo, Simona E. Rombo, Alberto Apostolico, Laxmi Parida

Research output: Contribution to journalArticlepeer-review

16 Citations (Scopus)

Abstract

Motif patterns consisting of sequences of intermixed solid and don't-care characters have been introduced and studied in connection with pattern discovery problems of computational biology and other domains. In order to alleviate the exponential growth of such motifs, notions of maximal saturation and irredundancy have been formulated, whereby more or less compact subsets of the set of all motifs can be extracted, that are capable of expressing all others by suitable combinations. In this paper, we introduce the notion of maximal irredundant motifs in a two-dimensional array and develop initial properties and a combinatorial argument that poses a linear bound on the total number of such motifs. The remainder of the paper presents approaches to the discovery of irredundant motifs both by offline and incremental algorithms.
Original languageEnglish
Pages (from-to)40-55
Number of pages15
JournalTheoretical Computer Science
Volume390
Publication statusPublished - 2008

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • General Computer Science

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