Easy identification of generalized common and conserved nested intervals

Abstract : In this paper we explain how to easily compute gene clusters, formalized by classical or generalized nested common or conserved intervals, between a set of K genomes represented as K permutations. A b-nested common (resp. conserved) interval I of size |I| is either an interval of size 1 or a common (resp. conserved) interval that contains another b-nested common (resp. conserved) interval of size at least |I|-b. When b=1, this corresponds to the classical notion of nested interval. We exhibit two simple algorithms to output all b-nested common or conserved intervals between K permutations in O(Kn+nocc) time, where nocc is the total number of such intervals. We also explain how to count all b-nested intervals in O(Kn) time. New properties of the family of conserved intervals are proposed to do so.
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Contributor : Fabien de Montgolfier <>
Submitted on : Saturday, December 21, 2013 - 12:44:38 AM
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Fabien de Montgolfier, Mathieu Raffinot, Irena Rusu. Easy identification of generalized common and conserved nested intervals. Journal of Computational Biology, Mary Ann Liebert, 2014, 21 (7), pp.520-533. ⟨10.1089/cmb.2013.0146⟩. ⟨hal-00921762⟩



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