Easy Identification of Generalized Common and Conserved Nested Intervals
نویسندگان
چکیده
منابع مشابه
Easy Identification of Generalized Common and Conserved Nested Intervals
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 ...
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Common intervals of K permutations over the same set of n elements were firstly investigated by T. Uno and M.Yagiura (Algorithmica, 26:290:309, 2000), who proposed an efficient algorithm to find common intervals when K = 2. Several particular classes of intervals have been defined since then, e.g. conserved intervals and nested common intervals, with applications mainly in genome comparison. Ea...
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In this article, we study the problem of efficiently finding gene clusters formalized by nested common intervals between two genomes represented either as permutations or as sequences. Considering permutations, we give several algorithms whose running time depends on the size of the actual output rather than the output in the worst case. Indeed, we first provide a straightforward cubic time alg...
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A bstract . The function h (z ) = ~ (z l i z ) is t he ewton map associated with the quadratic polynomial z 2 +1. The iterated dynamics of f on 3{ is usually st udied by exploit ing the conjugacy between f and the funct ion z f-> z2 In this paper we show how to use the technique of nested intervals t o yield a direct ana lysis of t he dynamics. We also show how to use the same technique to anal...
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ved. In this paper we consider the problem of finding common intervals of trees, a generalization of the concept of common intervals in permutations. For a permutation π of [n] = {1,2, . . . , n}, an interval of π is a set of the form {π(i),π(i + 1), . . . , π(j)} for 1 i < j n, and any permutation of [n] has n(n−1)/2 intervals. Given a family Π = (π0, . . . , πk−1) of k 2 permutations of [n], ...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2014
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2013.0146