Python for Bioinformatics

12 Multiple Sequence Alignment

Aligning two sequences is a relatively straightforward process, but aligning multiple sequences adds a new complication. There are two types of approaches: (1) the greedy approach, which attempts to find the best pairs of sequences that align and to build on those alignments, and (2) the nongreedy approach, which attempts to find the best group of alignments. The advantages of the greedy approach are that the programming is not too complicated and the system runs fast. The advantage of the nongreedy system is that the answer is usually better.

12.1 The Greedy Approach

A common sequencing project begins with a very long strand of DNA. Because sequencing machines have a short limit on the number of consecutive bases ...