In examining the functional aspects of the language of biological sequences, it becomes important to set out more precisely the goals of a language-theoretic approach. There are at least four broad roles for the tools and techniques of linguistics in this domain: specification, recognition, theory formation, and abstraction.
By specification we mean the use of formalisms such as grammars to indicate in a mathematically and computationally precise way the nature and relative locations of features in a sequence. Such a specification may be partial, only serving to constrain the possibilities with features that are important to one aspect of the system.
For example, published diagrams of genes typically only point out landmarks such as signal sequences, direct and inverted repeats, coding regions, and perhaps important restriction sites, all of which together clearly do not completely define any gene. However, a formal basis for such descriptions could serve to establish a lingua franca for interchange of information, and a similar approach may even extend to description of sequence analysis algorithms, as will be seen in a later section.
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Moreover, such high-level descriptions can merge into the second role for linguistics, that of recognition. This simply refers to the use of grammars as input to parsers which are then used for pattern-matching search—that is, syntactic pattern recognition—of what may be otherwise uncharacterized genomic sequence data.
We have seen that, in practice, these uses of linguistic tools tend to depart from the purely formal, for reasons of efficiency, yet a continued cognizance of the language-theoretic foundations can be important.
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