String variable grammar: A logic grammar formalism for the biological language of DNA

David B. Searls
1995 The Journal of Logic Programming  
~> Building upon Definite Clause Grammar (DCG), a number of logic grammar systems have been developed that are well-suited to phenomena in natural language. We have proposed an extension called String Variable Grammar (SVG), specifically tailored to the biological language of DNA. We here rigorously define and characterize this formalism, showing that it specifies a class of languages that properly contains the context-free languages, but is properly contained in the indexed languages. We give
more » ... number of mathematical and biological examples, and use an SVG variant to propose a new abstraction of the process of gene expression. A practical implementation called GF_~LANG is described, and some recent results in parsing genes and other high-level features of DNA sequences are summarized. <~
doi:10.1016/0743-1066(95)00034-h fatcat:jzz5ibw7szhg7ef6k6ch7gc2sa