Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection

Algorithm 5

Graph splitting algorithm.

(1)   function split_and_solve(globalGraph)

(2)   INPUT: globalGraph, an alignment graph between atoms from two proteins

(3)   OUTPUT: globalRes, a list of the longest distinct alignments found in the graph

(4)   

(5)   ResultList globalRes = empty_result_list()

(6)   Graph subGraphs = split(globalGraph)

(7)   sort(subgraphs)

(8)   For each subGraph in subGraphs

(9)      SeedList best_seeds = empty_list()

(10)    SeedList seeds = enumerate_seeds(subGraph)

(11)     For each seed in seeds

(12)       VertexSet current_res = extend_and_filter(subGraph, seed)

(13)       best_seeds.insert_if_better(seed)

(14)    End For

(15)    For each seed in best_seeds

(16)       VertexSet current_res = extend_and_filter(globalGraph, seed)

(17)       globalRes.insert_if_better(current_res)

(18)    End For

(19) End For