{"type":"ScholarlyArticle","title":"Efficient Dominant Point Algorithms for the Multiple Longest Common Subsequence (MLCS) Problem","authors":[{"name":"Qingguo Wang","slug":"qingguo-wang","given":"Qingguo","family":"Wang","affiliation":""},{"name":"Dmitry Korkin","slug":"dmitry-korkin","given":"Dmitry","family":"Korkin","affiliation":""},{"name":"Yi Shang","slug":"yi-shang","given":"Yi","family":"Shang","affiliation":""}],"abstract":"Finding the longest common subsequence of multiple strings is a classical computer science problem and has many applications in the areas of bioinformatics and computational genomics. In this paper, we present a new sequential algorithm for the general case of MLCS problem, and its parallel realization. The algorithm is based on the dominant point approach and employs a fast divide-and-conquer technique to compute the dominant points. When applied to find a MLCS of 3 strings, our general algorithm is shown to exhibit the same performance as the best existing MLCS algorithm by Hakata and Imai, designed specifically for the case of 3 strings. Moreover, we show that for a general case of more than 3 strings, the algorithm is significantly faster than the best existing sequential approaches, reaching up to 2-3 orders of magnitude faster on the large-size problems. Finally, we propose a parallel implementation of the algorithm. Evaluating the parallel algorithm on a benchmark set of both random and biological sequences reveals a near-linear speed-up with respect to the sequential algorithm.Qingguo Wang, Dmitry Korkin, Yi Shang","doi":null,"url":"https://ijcai.org/proceedings/2009/250","pdf":"https://ijcai.org/proceedings/2009/0250.pdf","markdown":"https://ijcai.org/proceedings/2009/250.md","bibtex":"https://ijcai.org/proceedings/2009/bibtex/250","volume":{"slug":"2009","title":"Proceedings of the Twenty-First International Joint Conference on Artificial Intelligence","short_title":"IJCAI 2009","url":"https://ijcai.org/proceedings/2009/","year":2009,"location":"Pasadena, California, USA","dates":"","editors":"Hiroaki Kitano","isbn":"","publisher":"International Joint Conferences on Artificial Intelligence","doi_prefix":""},"section":null,"track":"","number":250,"pages":{"first":1494,"last":1499},"keywords":[],"videos":[],"references":[],"license_note":"Copyright International Joint Conferences on Artificial Intelligence."}