TY - JOUR
AB - 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.
AU - Tönges, Udo
AU - Perrey, Sören W.
AU - Stoye, Jens
AU - Dress, Andreas
ID - 1773351
IS - 1
JF - Gene
KW - Secondary matrix
KW - Pair-wise sequence alignment
KW - Divide and conquer
KW - Multiple sequence alignment
KW - Dynamic programming
SN - 0378-1119
TI - A general method for fast multiple sequence alignment
VL - 172
ER -