J. Comput. Biol. - Easy identification of generalized common and conserved nested intervals.

Tópicos

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Resumo

In this article 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.

Resumo Limpo

articl explain easili comput gene cluster formal classic general nest common conserv interv set k genom repres k permut bnest common resp conserv interv size either interv size common resp conserv interv contain anoth bnest common resp conserv interv size least ib b correspond classic notion nest interv exhibit two simpl algorithm output bnest common conserv interv k permut oknnocc time nocc total number interv also explain count bnest interv okn time new properti famili conserv interv propos

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