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Bioinformatics Vol. 19 no. 12 2003
Pages 1497-1504
© 2003 Oxford University Press

Greedy method for inferring tandem duplication history

Louxin Zhang 1,*, Bin Ma 2, Lusheng Wang 3 and Ying Xu 4

1 Department of Mathematics, National University of Singapore, Singapore
2 Department of Computer Science, University of Western Ontario, Canada N6A 5B8
3 Department of Computer Science, City University of Hong Kong, Hong Kong
4 Department of Computer Science, Peking University, People’s Republic of China

Received on November 4, 2002 ; revised on November 18, 2002 ; accepted on February 18, 2003

Motivation: Genome analysis suggests that tandem duplication is an important mode of evolutionary novelty by permitting one copy of each gene to drift and potentially to acquire a new function. With more and more genomic sequences available, reconstructing duplication history has received extensive attention recently.

Results: An efficient method is presented for inferring the duplication history of tandemly repeated sequences based on the model proposed by Fitch (1977). We validate the method by using simulation results and real data sets of mucin genes, ZNF genes, and olfactory receptors genes. The agreement with conclusions drawn by other biological researchers strongly indicates that our method is efficient and robust.

Availability:The program is available by request.

Contact: matzlx{at}nus.edu.sg

* To whom correspondence should be addressed.


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