Algorithms for Loosely Constrained Multiple Sequence Alignment

Abstract

For finding accurate and biologically meaningful multiple sequence alignment, it is required to consider a loosely constrained version of multiple sequence alignment. This paper is the first to define a loosely constrained multiple sequence alignment (LCMSA). And it also designs a complete algorithm for the loosely constrained pair-wise sequence alignment problem with the time complexity of O((α + 1)n ^{2(α + 1)}) and an approximation algorithm for LCMSA running in time O(k ²(α + 1)n ^{2(α + 1)}), k and n is the number and the maximum length of input sequences, and α is the length of constrained sequence. In fact, α is small compared to n and it is reasonable to regard it as a constant. So, the former two algorithms run in polynomial time. Finally, a LCMSA software system is built up.

This work was supported by the National ‘863’ High-Tech Program of China under the grant No.2001AA111041, 2002AA104560, and High-standard Universities Construction Project in CAS.