@article{1773351,
abstract = {We have developed a fast heuristic algorithm for multiple sequence alignment which provides near-to-optimal results for sufficiently homologous sequences. The algorithm makes use of the standard dynamic programming procedure by applying it to all pairs of sequences. The resulting score matrices for pair-wise alignment give rise to secondary matrices containing the additional charges imposed by forcing the alignment path to run through a particular vertex. Such a constraint corresponds to slicing the sequences at the positions defining that vertex, and aligning the remaining pairs of prefix and suffix sequences separately. From these secondary matrices, one can compute - for any given family of sequences - suitable positions for cutting all of these sequences simultaneously, thus reducing the problem of aligning a family of n sequences of average length l in a Divide and Conquer fashion to aligning two families of n sequences of approximately half that length. In this paper, we explain the method for the case of 3 sequences in detail, and we demonstrate its potential and its limits by discussing its behaviour for several test families. A generalization for aligning more than 3 sequences is lined out, and some actual alignments constructed by our algorithm for various user-defined parameters are presented.},
author = {Tönges, Udo and Perrey, Sören W. and Stoye, Jens and Dress, Andreas},
issn = {0378-1119},
journal = {Gene},
keyword = {Secondary matrix, Pair-wise sequence alignment, Divide and conquer, Multiple sequence alignment, Dynamic programming},
number = {1},
pages = {GC33--GC41},
title = {{A general method for fast multiple sequence alignment}},
doi = {10.1016/0378-1119(96)00123-0},
volume = {172},
year = {1996},
}