Paper Info
Title
String variable grammar: A logic grammar formalism for the biological language of DNA
Abstract
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 a 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 GenLang is described, and some recent results in parsing genes and other high-level features of DNA sequences are summarized.
Year
DOI
Venue
1995
10.1016/0743-1066(95)00034-H
The Journal of Logic Programming
Keywords
Field
DocType
gene expression,context free language,definite clause grammar,dna sequence,natural language,indexation
Attribute grammar,Programming language,Computer science,Operator-precedence grammar,Artificial intelligence,Natural language processing,Regular grammar,Mildly context-sensitive grammar formalism,Algorithm,Emergent grammar,Adaptive grammar,Affix grammar,Generative grammar
Journal
Volume
Issue
ISSN
24
1
0743-1066
Citations 
PageRank 
References 
32
8.52
10
Authors
1
Name
Order
Citations
PageRank
David B. Searls1314171.53