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Online Lectures on Bioinformatics


Pairwise sequence comparison


The methods of the last section (Individual sequence analysis) analyzed a sequence by its own virtues. We now turn to the comparison of two sequences. The rationales behind the comparison of sequences may be manifold. Above all, the theory of evolution tells us that gene sequences may have derived from common ancestral sequences. Thus it is of interest to trace the evolutionary history of mutations and other evolutionary changes. Comparison of biological sequences in this context is understood as comparison based on the criteria of evolution. For example, the number of mutations, insertions, and deletions of bases necessary to transform one DNA sequence into another one is a measure reflecting evolutionary relatedness.

On the other hand, a comparison may be more pragmatic in that it is not aimed at a detailed reconstruction of the evolutionary course of events but rather aims at pinpointing regions of common origin which may in turn coincide with regions of similar structure or similar function. Physical characteristics of amino acids play a more important role in this viewpoint than they do when studying evolution.

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