Simple operations for gene assembly

  • Authors:

  • Tero Harju;Ion Petre;Vladimir Rogojin;Grzegorz Rozenberg

  • Affiliations:

  • Department of Mathematics, University of Turku, Turku, Finland;Academy of Finland;Department of Computer Science, Åbo Akademi University, Turku, Finland;Leiden Institute for Advanced Computer Science, Leiden University, Leiden, The Netherlands

  • Venue:
  • DNA'05 Proceedings of the 11th international conference on DNA Computing
  • Year:
  • 2005

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Abstract

The intramolecular model for gene assembly in ciliates considers three operations, ld, hi, and dlad that can assemble any gene pattern through folding and recombination: the molecule is folded so that two occurrences of a pointer (short nucleotide sequence) get aligned and then the sequence is rearranged through recombination of pointers. In general, the sequence rearranged by one operation can be arbitrarily long and consist of many coding and non-coding blocks. We consider in this paper some simpler variants of the three operations, where only one coding block is rearranged at a time. We characterize in this paper the gene patterns that can be assembled through these variants. Our characterization is in terms of signed permutations and dependency graphs. Interestingly, we show that simple assemblies possess rather involved properties: a gene pattern may have both successful and unsuccessful assemblies and also more than one successful assembling strategy.