Multiple Sequence Alignment

5.4 Summary

Multiple sequence alignments are often computed for known members of a protein family. The aim is to discover sequence motifs that are conserved across the mem bers of the protein family in order to infer the functionally important protein domains. Like pairwise sequence alignments, multiple sequence alignments can be computed using optimal or heuristic methods. In practice most multiple sequence alignments are computed using heuristic methods. These proceed by reducing the multiple alignment problem to a series of pairwise alignments. The order in which these pairwise alignments are fused into the multiple alignment is crucial for the success of the algorithm. The pairwise alignments of the input sequences are used to calculate pairwise distances. This in turn serves as input data for the construction of a guide tree, which determines the order in which sequences are added to the multiple alignment.