Sequence Alignment Algorithms for Run-Length-Encoded Strings

A unified framework is applied to solving various sequence comparison problems for run-length encoded strings. All of these algorithms take O(min{mn , m n}) time and O(max{m, n}) space, for two strings of lengths m and n, with m and n runs, respectively. We assume the linear-gap model and make no assumption on the scoring matrices, which maximizes the applicability of these algorithms. The trace (i.e., the way to align two strings) of an optimal solution can also be recovered within the same time and space bounds.

• Type: Conference
• Year: 2008
• Where: COCOON
• Authors: Guan-Shieng Huang, Jia Jie Liu, Yue-Li Wang
• Keywords: COCOON 2008, Combinatorics, Run-length Encoded Strings, Sequence Comparison Problems, Unified Framework