Polynomial-time algorithm for computing translocation distance between genomes
Discrete Applied Mathematics - Special volume on computational molecular biology
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
Of mice and men: algorithms for evolutionary distances between genomes with translocation
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Transforming men into mice (polynomial algorithm for genomic distance problem)
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
An O(n2) algorithm for signed translocation
Journal of Computer and System Sciences - Special issue on bioinformatics II
An O(n3/2√log(n)) algorithm for sorting by reciprocal translocations
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
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Translocation is a prevalent rearrangement event in the evolution of multi-chromosomal species which exchanges ends between two chromosomes. A translocation is reciprocal if none of the exchanged ends is empty; otherwise, non-reciprocal. The problem of sorting by translocations asks to find a shortest sequence of translocations transforming one genome into another. The problem of sorting by reciprocal translocations can be solved in polynomial-time. Several algorithms have been developed for reciprocal translocation sorting. They can only be applied to a pair of genomes having the same set of chromosome ends. Such a restriction can be removed if non-reciprocal translocations are also allowed. In this paper, we show how to extend the algorithm for sorting by reciprocal translocations to include non-reciprocal translocations, allowing us to compare genomes containing different chromosome ends. We call this problem sorting by generalized translocations. We present a polynomial algorithm for this problem. At a conceptual level, there is some similarity between our algorithm and the algorithm developed by Hannenhalli which is used to sort genomes by reversals and translocations.