Comparing Genomes with Duplications: A Computational Complexity Point of View
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The ExemplarBreakpointDistance for Non-trivial Genomes Cannot Be Approximated
WALCOM '09 Proceedings of the 3rd International Workshop on Algorithms and Computation
Approximability and Fixed-Parameter Tractability for the Exemplar Genomic Distance Problems
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
A polynomial algebra method for computing exemplar breakpoint distance
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Maximizing synteny blocks to identify ancestral homologs
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
A framework for orthology assignment from gene rearrangement data
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
The approximability of the exemplar breakpoint distance problem
AAIM'06 Proceedings of the Second international conference on Algorithmic Aspects in Information and Management
Lower bounds on the approximation of the exemplar conserved interval distance problem of genomes
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
Non-breaking similarity of genomes with gene repetitions
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
An Exact Algorithm for the Zero Exemplar Breakpoint Distance Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: A one-to-one correspondence between the sets of genes in the two genomes being compared is necessary for the notions of breakpoint and reversal distances. To compare genomes where there are paralogous genes, Sankoff formulated the exemplar distance problem as a general version of the genome rearrangement problem. Unfortunately, the problem is NP-hard even for the breakpoint distance. Results: This paper proposes a divide-and-conquer approach for calculating the exemplar breakpoint distance between two genomes with multiple gene families. The combination of our approach and Sankoff's branch-and-bound technique leads to a practical program to answer this question. Tests with both simulated and real datasets show that our program is much more efficient than the existing program that is based only on the branch-and-bound technique. Availability: Code for the program is available from the authors. Contact: matzlx@nus.edu.sg