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.
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