An improved voting algorithm for planted (l, d) motif search

The planted motif search problem is a classical problem in bioinformatics that seeks to identify meaningful patterns in biological sequences. As an NP-complete problem, current algorithms focus on improving the average time complexity and solving challenging instances within an acceptable time. In this paper, we propose a new exact algorithm CVoting that improves the state-of-the-art Voting algorithm. CVoting uses a new hash technique to reduce the space complexity to O(mn + N(l, d  )) and a new pruning technique to reduce the average time complexity to Om2nN(l,d)14+3ll. Experimental results show that CVoting outperforms competing algorithms, including PMS1, RISOTTO, Voting and Pmsprune, in both space and time: up to an order of magnitude faster and using less memory in solving challenging instances. The software of the proposed algorithm is publicly available at http://staff.ustc.edu.cn/xuyun/motif.