A New Efficient Algorithm for the Gene-Team Problem on General Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Output-Sensitive Algorithms for Finding the Nested Common Intervals of Two General Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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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, B茅al et al. had an O(n{\rm lg}^2n)-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}^2n)-time algorithm. Our improved algorithm requires O(n{\rm lg} n{\rm lglg} n) time. Similar to B茅al 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.