Motif patterns in 2D

  • Authors:

  • Alberto Apostolico;Laxmi Parida;Simona E. Rombo

  • Affiliations:

  • College of Computing, Georgia Institute of Technology, 801 Atlantic Dr., Atlanta 30332, GA, USA and Department of Information Engineering, University of Padua, via Gradenigo, 6/A, I-35131 Padova, ...;IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, USA;DEIS, University of Calabria, via P. Bucci, 87036 Arcavacata di Rende, CS, Italy

  • Venue:
  • Theoretical Computer Science
  • Year:
  • 2008

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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.