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Issue No. 02 - March-April (2013 vol. 10)
ISSN: 1545-5963
pp: 504-513
Ali Gholami Rudi , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
Saeed Shahrivari , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
Saeed Jalili , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
Zahra Razaghi Moghadam Kashani , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
ABSTRACT
Given a multiset of colors as the query and a list-colored graph, i.e., an undirected graph with a set of colors assigned to each of its vertices, in the NP-hard list-colored graph motif problem the goal is to find the largest connected subgraph such that one can select a color from the set of colors assigned to each of its vertices to obtain a subset of the query. This problem was introduced to find functional motifs in biological networks. We present a branch-and-bound algorithm named RANGI for finding and enumerating list-colored graph motifs. As our experimental results show, RANGI's pruning methods and heuristics make it quite fast in practice compared to the algorithms presented in the literature. We also present a parallel version of RANGI that achieves acceptable scalability.
INDEX TERMS
Color, Heuristic algorithms, Computational biology, Bioinformatics, Proteins
CITATION

A. G. Rudi, S. Shahrivari, S. Jalili and Z. R. Moghadam Kashani, "RANGI: A Fast List-Colored Graph Motif Finding Algorithm," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 2, pp. 504-513, 2013.
doi:10.1109/TCBB.2012.167
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