Multiple Sequence Alignment

Insertion of gaps to optimize the alignment among 3 or more sequences

Objectives:

Determine whether a group of proteins are related
Show regions of conservation within a protein
Determine the number of ortholgous groups within a multigene familiy
Determine evolutionary history of a gene family
Determine evolutionary relationships among species or populations

Efficiency (dynamic programming): O(k²2^kn^k)

Constructing Multiple Alignments

Cluster based methods are still an approximation with no guarantee of being optimal.

Alignment is strongly biased toward tree, but any phylogenetic tree implicitly assumes some multiple alignment.

http://home.cc.umanitoba.ca/~frist/Seminars/iims02/iims02.html