Algorithms for Finding Gene Clusters

  • Steffen Heber
  • Jens Stoye
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2149)


Comparing gene orders in completely sequenced genomes is a standard approach to locate clusters of functionally associated genes. Often, gene orders are modeled as permutations. Given k permutations of n elements, a k-tuple of intervals of these permutations consisting of the same set of elements is called a common interval. We consider several problems related to common intervals in multiple genomes. We present an algorithm that finds all common intervals in a family of genomes, each of which might consist of several chromosomes. We present another algorithm that finds all common intervals in a family of circular permutations. A third algorithm finds all common intervals in signed permutations. We also investigate how to combine these approaches. All algorithms have optimal worst-case time complexity and use linear space.


Gene Order Circular Chromosome Additional Space Active Interval Circular Permutation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • Steffen Heber
    • 1
  • Jens Stoye
    • 2
  1. 1.Department of Computer Science & EngineeringUniversity of CaliforniaSan Diego
  2. 2.Max Planck Institute for Molecular GeneticsBerlinGermany

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