A Survey on Syntactic Pattern Recognition Methods in Bioinformatics

Invited paper

Abstract

Formal tools and models of syntactic pattern recognition which are used in bioinformatics are introduced and characterized in the paper. They include, among others: stochastic (string) grammars and automata, hidden Markov models, programmed grammars, attributed grammars, stochastic tree grammars, Tree Adjoining Grammars (TAGs), algebraic dynamic programming, NLC- and NCE-type graph grammars, and algebraic graph transformation systems. The survey of applications of these formal tools and models in bioinformatics is presented.