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Bioinformatics Advance Access published online on February 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti327
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 3, 2004
Revised February 5, 2005
Accepted February 10, 2005

Article

Divide-and-conquer approach for the exemplar breakpoint distance

C. Thach Nguyen 1*, Y. C. Tay 2, and Louxin Zhang 3

1 School of Computing, National University of Singapore, Singapore 117543
2 School of Computing, National University of Singapore, Singapore 117543; Department of Mathematics, National University of Singapore, Singapore 117543
3 Department of Mathematics, National University of Singapore, Singapore 117543

* To whom correspondence should be addressed.
C. Thach Nguyen, E-mail: matzlx{at}nus.edu.sg


  Abstract

Motivation: A one-to-one correspondence between the sets of genes in the two genomes being compared is necessary to 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 NPhard 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 our program is available from the authors.


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