The Language Metaphor in Sequence Analysis

Abstract The metaphors of language and coding have provided a powerful framework for organizing molecular biology. Many techniques developed in the analysis of text and other communication channels hasve been successfully applied to macromolecular sequences with little or no change. However, a number of properties, such as long-range interactions, structural dynamics and the importance of sequence variation in modulation of function, are poorly modelled by the language metaphor. It is not necessary to abandon the power of the language metaphor, but it is suggested that a conscious effort to set aside this compelling metaphor and examine other viewpoints is likely to be useful.

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