a new, fast algorithm for detecting protein coevolution using maximum compatible cliques一个新的、快速检测蛋白质共同进化算法使用最大派系兼容.pdfVIP

Rodionov et al. Algorithms for Molecular Biology 2011, 6:17 /content/6/1/17 RESEARCH Open Access A new, fast algorithm for detecting protein coevolution using maximum compatible cliques 1* 2 1 2,3* Alex Rodionov , Alexandr Bezginov , Jonathan Rose and Elisabeth RM Tillier Abstract Background: The MatrixMatchMaker algorithm was recently introduced to detect the similarity between phylogenetic trees and thus the coevolution between proteins. MMM finds the largest common submatrices between pairs of phylogenetic distance matrices, and has numerous advantages over existing methods of coevolution detection. However, these advantages came at the cost of a very long execution time. Results: In this paper, we show that the problem of finding the maximum submatrix reduces to a multiple maximum clique subproblem on a graph of protein pairs. This allowed us to develop a new algorithm and program implementation, MMMvII, which achieved more than 600× speedup with comparable accuracy to the original MMM. Conclusions: MMMvII will thus allow for more more extensive and intricate analyses of coevolution. Availability: An implementation of the MMMvII algorithm is available at: http://www.uhnresearch.ca/labs/tillier/ MMMWEBvII/MMMWEBvII.php Background each others’ rate of evolution such that these are more An important problem in evolutionary biology is the likely to evolve with correlated rates – a process known comparison of phylogenetic trees [1]. Tree comparisons as coevolution. Proteins that coevolve have similar evolu- have been performed to establish the accuracy of phylo- tionary histories, in terms o