Publication 2011 Issue No. 5 - September/October Abstract - Improved Algorithms for Finding Gene Teams and Constructing Gene Team Trees
Improved Algorithms for Finding Gene Teams and Constructing Gene Team Trees
September/October 2011 (vol. 8 no. 5)
pp. 1258-1272
 ASCII Text x 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.
 BibTex x @article{ 10.1109/TCBB.2010.127,author = {Biing-Feng Wang and Chien-Hsin Lin},title = {Improved Algorithms for Finding Gene Teams and Constructing Gene Team Trees},journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},volume = {8},number = {5},issn = {1545-5963},year = {2011},pages = {1258-1272},doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.127},publisher = {IEEE Computer Society},address = {Los Alamitos, CA, USA},}
 RefWorks Procite/RefMan/Endnote x TY - JOURJO - IEEE/ACM Transactions on Computational Biology and BioinformaticsTI - Improved Algorithms for Finding Gene Teams and Constructing Gene Team TreesIS - 5SN - 1545-5963SP1258EP1272EPD - 1258-1272A1 - Biing-Feng Wang, A1 - Chien-Hsin Lin, PY - 2011KW - AlgorithmsKW - data structuresKW - gene teamsKW - comparative genomicsKW - conserved gene clusters.VL - 8JA - IEEE/ACM Transactions on Computational Biology and BioinformaticsER -
Biing-Feng Wang, National Tsing Hua University, Hsinchu
Chien-Hsin Lin, National Tsing Hua University, Hsinchu
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.

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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, Sept.-Oct. 2011, doi:10.1109/TCBB.2010.127