Computing Nonoverlapping Inversion Distance Between Two Strings in Linear Average Time

Journal of computational biology: A journal of computational molecular cell biology

XiaodongWang^1,2¹  LeiWang^3,4² 

[1] Address correspondence to: Prof. Xiaodong Wang, Computer Science Department, Fujian University of Technology, Fuzhou 350118, China^1;Computer Science Department, Fujian University of Technology, Fuzhou, China^2;Dr. Lei Wang, Facebook, Inc., Menlo Park, CA 94052^3;Facebook, Inc., Menlo Park, California^4

关键词: algorithms;    combinatorics;    optimization;   

DOI  :  10.1089/cmb.2018.0136

学科分类：生物科学（综合）

来源: Mary Ann Liebert, Inc. Publishers

【 摘 要 】

Biological events like inversions are not automatically detected by the usual alignment algorithms. Alignment with inversions does not have a known polynomial time algorithm and Schöniger and Waterman introduced a simplification of the alignment problem with nonoverlapping inversions, where all regions will not be allowed to overlap. They presented analgorithm to compute nonoverlapping inversion distance between two strings of length n. The time and space complexities were improved toandlater by Cho, Vellozo, and Ta. In this article, a linear space and linear average time algorithm to compute the inversion distance between two strings of the same length is presented. The recursive formula for this purpose is new to the best of our knowledge. The space costs of the algorithms to solve the same problem are quadratic in the literature, and thus our original algorithm is the first linear space and linear average time algorithm to solve the inversion distance problem.

【 授权许可】

Unknown