Algorithms for Loosely Constrained Multiple Sequence Alignment

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)n2(α+1) ) and an approximation algorithm for LCMSA running in time O(k2 (α+1)n2(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.

• Type: Conference
• Year: 2004
• Where: CIS
• Authors: Bin Song, Fengfeng Zhou, Guoliang Chen
• Keywords: CIS 2004, Meaningful Multiple Sequence, Multiple Sequence Alignment, Sequence Alignment