B. Ma, L. Wang, M. Li, Fixed topology alignment with recombination. Discrete Applied Math. (Special Issue on Computational Molecular Biology), 104(2000), 281-300. Home/Search Document Details and Download
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A Greedy Algorithm for Optimal Recombination - Wu, Gu (2001) (Correct)
....and its aim is to find the optimal evolutionary history from some ancestors to some descendents by using certain types of mutations such as insertion, deletion, substitution (point mutation) reversal, etc. Parsimony trees and phylogenetic trees are some intersting problems in the category. In [6], an alignment with recombination is discussed and it is an edit distance problem involved recombinations. In this paper, we discuss a similar distance problem involved recombinations. The purpose is to generate a collection A of sequences from another collection S of sequences by a series of ....
....we define a recombination consisting of a single crossover with no point mutations. We discuss a more general problem to construct the optimal recombination spanning history from one family of sequences to another one. Its general case with multiple crossovers and point mutations is NP complete(cf.[5, 6]) 2 Theorems and algorithms In this section, we show some theorems on optimal recombination processes and design a greedy algorithm for finding the optimal recombination process for a tree of binary sequences. We always assume S = f00 Delta Delta Delta 0; 11 Delta Delta Delta 1g: Theorem ....
Wang,L., B. Ma and M. Li, 2000, Fixed topology alignment with recombination, Discrete Applied Mathematics 104: 281-300
Selected Topics in Computational Biology - DasGupta, Wang (1998) Self-citation (Wang) (Correct)
....is that the given topology is no longer a binary tree. Instead, there are some recombination nodes which have two parents instead of one. Moreover, there may be more than one root in the topology. A different version called fixed topology alignment with recombination (FTAR) is also dicsussed [53]. From approximation point of view, FTHR and FTAR are much harder than tree alignment. It is shown that FTHR and FTAR cannot be approximated within any constant performance ratio unless P = NP [53] A more restricted case, where each internal node has at most one recombination child and there are ....
....A different version called fixed topology alignment with recombination (FTAR) is also dicsussed [53] From approximation point of view, FTHR and FTAR are much harder than tree alignment. It is shown that FTHR and FTAR cannot be approximated within any constant performance ratio unless P = NP [53]. A more restricted case, where each internal node has at most one recombination child and there are at most 6 parents of recombination nodes in any path from the root to a leaf in the given topology, is also considered. It is shown that the restricted version for both FTHR and FTAR is ....
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B. Ma, L. Wang and M. Li. Fixed topology alignment with recombination, CPM98, to appear.
Multiple Genome Rearrangement By Reversals - Wu, Gu (2002) (Correct)
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Wang,L., B. Ma and M. Li, 2000, Fixed topology alignment with recombination, Discrete Applied Mathematics 104: 281-300
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