Basic Gene Grammars and DNA Chart Parser for Language Processing of Escherichia Coli promoter DNA

S. Leung, Christopher Stuart Mellish, D. Robertson

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

Motivation: The field of 'DNA linguistics' has emerged from pioneering work in computational linguistics and molecular biology. Most formal grammars in this field are expressed using Definite Clause Grammars but these have computational limitations which must be overcome. The present study provides a new DNA parsing system, comprising a logic grammar formalism called Basic Gene Grammars and a bidirectional chart parser DNA-ChartParser.

Results: The use of Basic Gene Grammars is demonstrated in representing many formulations of the knowledge of Escherichia coli promoters, including knowledge acquired from human experts, consensus sequences, statistics (weight matrices), symbolic learning, and neural network learning. The DNA-ChartParser provides bidirectional parsing facilities for BGGs in handling overlapping categories, gap categories, approximate pattern matching, and constraints. Basic Gene Grammars and the DNA-ChartParser allowed different sources of knowledge for recognizing E,coli promoters to be combined to achieve better accuracy as assessed by parsing these DNA sequences in real-world data sets.

Availability: DNA-ChartParser runs under SICStus Prolog. It and a few examples of Basic Gene Grammars are available at the URL: http://www.dai.ed.ac.uk/-siu/DNA.

Original languageEnglish
Pages (from-to)226-236
Number of pages10
JournalBioinformatics
Volume17
Issue number3
DOIs
Publication statusPublished - Jan 2001

Keywords

  • NEURAL NETWORKS
  • KNOWLEDGE
  • LINGUISTICS
  • RECOGNITION
  • EXPRESSION
  • SEARCH

Cite this

Basic Gene Grammars and DNA Chart Parser for Language Processing of Escherichia Coli promoter DNA. / Leung, S.; Mellish, Christopher Stuart; Robertson, D.

In: Bioinformatics, Vol. 17, No. 3, 01.2001, p. 226-236.

Research output: Contribution to journalArticle

Leung, S. ; Mellish, Christopher Stuart ; Robertson, D. / Basic Gene Grammars and DNA Chart Parser for Language Processing of Escherichia Coli promoter DNA. In: Bioinformatics. 2001 ; Vol. 17, No. 3. pp. 226-236.
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