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
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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(k22knk)
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