title: PALM--a pattern language for molecular biology.
abstract: This paper presents a new pattern language, PALM, for describing patterns in molecular biology sequences. The language is intended for representing knowledge about such patterns in a declarative, clear and concise way. It is also shown that its expressive power enables the definition of any regular or context free language, and also higher languages in the Chomsky hierarchy by parameter attachment, variables and procedural attachment. It is also possible to define approximate patterns. The language is rigorously defined, and several examples of its use and expressive power are given.
authors.affiliation: Department of Informatics, University of Bergen, Norway.
authors.forename: C
authors.initials: C
authors.lastname: Helgesen
authors.forename: P R
authors.initials: PR
authors.lastname: Sibbald
mesh_terms: D004259:DNA-Directed DNA Polymerase; D012321:DNA-Directed RNA Polymerases; D016208:Databases, Factual; D006025:Glycosaminoglycans; D008074:Lipoproteins; D008967:Molecular Biology / Q000379:methods*; D009323:Natural Language Processing; D009687:Nuclear Proteins; D010363:Pattern Recognition, Automated; D011381:Programming Languages; D017421:Sequence Analysis / Q000379:methods*; D013463:Sulfuric Acid Esters
chemical_list: D006025:Glycosaminoglycans; D008074:Lipoproteins; D009687:Nuclear Proteins; D013463:Sulfuric Acid Esters; D012321:DNA-Directed RNA Polymerases; D004259:DNA-Directed DNA Polymerase