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Issue No.05 - September/October (2011 vol.8)
pp: 1258-1272
Biing-Feng Wang , National Tsing Hua University, Hsinchu
Chien-Hsin Lin , National Tsing Hua University, Hsinchu
ABSTRACT
A gene team is a set of genes that appear in two or more species, possibly in a different order yet with the distance between adjacent genes in the team for each chromosome always no more than a certain threshold \delta. A gene team tree is a succinct way to represent all gene teams for every possible value of \delta. In this paper, improved algorithms are presented for the problem of finding the gene teams of two chromosomes and the problem of constructing a gene team tree of two chromosomes. For the problem of finding gene teams, Béal et al. had an O(n {\rm lg}^2 n)-time algorithm. Our improved algorithm requires O(n {\rm lg} t) time, where t \le n is the number of gene teams. For the problem of constructing a gene team tree, Zhang and Leong had an O(n {\rm lg}^2 n)-time algorithm. Our improved algorithm requires O(n {\rm lg} n {\rm lglg} n) time. Similar to Béal et al.'s gene team algorithm and Zhang and Leong's gene team tree algorithm, our improved algorithms can be extended to k chromosomes with the time complexities increased only by a factor of k.
INDEX TERMS
Algorithms, data structures, gene teams, comparative genomics, conserved gene clusters.
CITATION
Biing-Feng Wang, Chien-Hsin Lin, "Improved Algorithms for Finding Gene Teams and Constructing Gene Team Trees", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, no. 5, pp. 1258-1272, September/October 2011, doi:10.1109/TCBB.2010.127
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