SIAM Journal on Discrete Mathematics
A 2-approximation algorithm for genome rearrangements by reversals and transpositions
Theoretical Computer Science - Special issue: Genome informatics
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
Sorting Permutations by Reversals and Eulerian Cycle Decompositions
SIAM Journal on Discrete Mathematics
Signed genome rearrangement by reversals and transpositions: models and approximations
Theoretical Computer Science
Genome Rearrangements and Sorting by Reversals
SIAM Journal on Computing
(1 + ɛ)-Approximation of sorting by reversals and transpositions
Theoretical Computer Science
1.375-Approximation Algorithm for Sorting by Reversals
ESA '02 Proceedings of the 10th Annual European Symposium on Algorithms
A very elementary presentation of the Hannenhalli-Pevzner theory
Discrete Applied Mathematics
A simpler 1.5-approximation algorithm for sorting by transpositions
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Efficient data structures and a new randomized approach for sorting signed permutations by reversals
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
A 1.375-approximation algorithm for sorting by transpositions
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Whole genome duplications, multi-break rearrangements, and genome halving problem
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Multi-break rearrangements and chromosomal evolution
Theoretical Computer Science
Prefix reversals on binary and ternary strings
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Multi-break rearrangements: from circular to linear genomes
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient sampling of transpositions and inverted transpositions for bayesian MCMC
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Hi-index | 0.00 |
During evolution, genomes are subject to genome rearrangements that alter the ordering and orientation of genes on the chromosomes. If a genome consists of a single chromosome (like mitochondrial, chloroplast or bacterial genomes), the biologically relevant genome rearrangements are (1) inversions—also called reversals—where a section of the genome is excised, reversed in orientation, and reinserted and (2) transpositions, where a section of the genome is excised and reinserted at a new position in the genome; if this also involves an inversion, one speaks of an inverted transposition. To reconstruct ancient events in the evolutionary history of organisms, one is interested in finding an optimal sequence of genome rearrangements that transforms a given genome into another genome. It is well known that this problem is equivalent to the problem of “sorting” a signed permutation into the identity permutation. The complexity of the problem is still unknown. The best polynomial-time approximation algorithm, recently devised by Hartman and Sharan, has a 1.5 performance ratio. However, it applies only to the case in which reversals and transpositions are weighted equally. Because in most organisms reversals occur more often than transpositions, it is desirable to have the possibility of weighting reversals and transpositions differently. In this paper, we provide a 1.5-approximation algorithm for sorting by weighted reversals, transpositions and inverted transpositions for biologically realistic weights.