An efficient algorithm for pairwise local alignment of protein interaction networks

作者：Chen Wenbin^*; Schmidt Matthew; Tian Wenhong; Samatova Nagiza F; Zhang Shaohong

来源：Journal of Bioinformatics and Computational Biology, 2015, 13(2): 1550003.

DOI：10.1142/S0219720015500031

• Network alignment
• conserved functional modules
• graph optimization
• graph theory

Recently, researchers seeking to understand, modify, and create beneficial traits in organisms have looked for evolutionarily conserved patterns of protein interactions. Their conservation likely means that the proteins of these conserved functional modules are important to the trait's expression.
In this paper, we formulate the problem of identifying these conserved patterns as a graph optimization problem, and develop a fast heuristic algorithm for this problem. We compare the performance of our network alignment algorithm to that of the MaWISh algorithm [Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A, Pairwise alignment of protein interaction networks, J Comput Biol 13(2): 182-199, 2006.], which bases its search algorithm on a related decision problem formulation. We find that our algorithm discovers conserved modules with a larger number of proteins in an order of magnitude less time.
The protein sets found by our algorithm correspond to known conserved functional modules at comparable precision and recall rates as those produced by the MaWISh algorithm.

• 单位
  复旦大学; 广州大学; 南京大学