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C. Pairwise and Multiple Alignments

Pairwise alignment is the basis of similarity searching

Pairwise alignment has been "solved" as a computational problem = dynamic programming

The "optimal" alignment calculated by the computer is often not the best biological alignment.

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Multiple Sequence Alignments

Multiple Alignment is the basis for the study of protein families and functional domains.

When pairwise alignment is expanded to multiple sequences, it becomes a computationally huge problem.

To reduce the nearly infinite permutations, a simplified heuristic (approximate) algorithm is used known as progressive pariwise alignment

Since this problem is so complex, it is not possible to mathematically define a truly optimal alignment of multiple sequences.

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Using Computers for Molecular Biology
Stuart M. Brown, Ph.D., RCR, NYU Medical Center

Comments to: browns02@mcrcr.med.nyu.edu