Multiple sequence alignment with the divide-and-conquer method

Multiple sequence alignment with the Divide-and-Conquer method.

An improved algorithm for the simultaneous alignment of multiple protein and nucleic acid sequences, the Divide-and-Conquer Alignment procedure (DCA), is presented. The basic method described in Tönges,et al. (1996) (Tönges, U., Perrey, S.W., Stoye, J., Dress, A.W.M., 1996. A general method for fast multiple sequence alignment. Gene, 172, GC33-GC41) is generalized to align any number of sequenc...

Divide - and - Conquer Multiple Sequence

Divide-and-conquer multiple alignment with segment-based constraints

A large number of methods for multiple sequence alignment are currently available. Recent benchmarking tests demonstrated that strengths and drawbacks of these methods differ substantially. Global strategies can be outperformed by approaches based on local similarities and vice versa, depending on the characteristics of the input sequences. In recent years, mixed approaches that include both gl...

Divide-and-Conquer Frontier Search Applied to Optimal Sequence Alignment

We present a new algorithm that reduces the space complexity of heuristic search It is most e ective for problem spaces that grow polynomially with problem size but contain large numbers of short cycles For ex ample the problem of nding an optimal global align ment of several DNA or amino acid sequences can be solved by nding a lowest cost corner to corner path in a d dimensional grid A previou...

Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment

We consider the problem of multiple sequence alignment: given k sequences of length at most n and a certain scoring function, find an alignment that minimizes the corresponding “sum of pairs” distance score. We generalize the divide-and-conquer technique described in [1,2], and present new ideas on how to use efficient search strategies for saving computer memory and accelerating the procedure ...