Abstract
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.
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Heber, S., Stoye, J. (2001). Algorithms for Finding Gene Clusters. In: Gascuel, O., Moret, B.M.E. (eds) Algorithms in Bioinformatics. WABI 2001. Lecture Notes in Computer Science, vol 2149. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44696-6_20
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DOI: https://doi.org/10.1007/3-540-44696-6_20
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