Multiple Sequence Comparison and HMMs

A sequence family is a set of homologous sequences. Members of a sequence family diverge during evolution and share similarities, but similarities that span the entire family might be weak compared to similarities that span only few members of the family. When comparing any two members of the family the faint similarities that span the entire family are thus likely to be shadowed by the stronger similarities between the particular two members. To detect similarities that span an entire sequence family it is therefore advisable to use other methods than just pairwise comparisons of the members. Comparison of several sequences is a difficult problem that involves many modeling choices. The comparison of several sequences is typical communicated using a multiple alignment that express how the sequences relate by substitutions, insertions, and deletions. In this section we focus on methods to compute multiple alignments and ways to extract a compact characterization of a sequence family based on a comparison of its members. Such a characterization can be used to search for unknown members of the family, and for comparison against the characterizations of other families.