Informatics Report Series



Related Pages

Report (by Number) Index
Report (by Date) Index
Author Index
Institute Index

Title:Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences
Authors: Siu-wai Leung ; Chris Mellish ; Dave Robertson
Date: 2001
Publication Title:Bioinformatics
Publication Type:Journal Article Publication Status:Published
Volume No:17(3) Page Nos:226-236
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 DNAChartParser 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.
Links To Paper
1st link
Bibtex format
author = { Siu-wai Leung and Chris Mellish and Dave Robertson },
title = {Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences},
journal = {Bioinformatics},
publisher = {OUP},
year = 2001,
volume = {17(3)},
pages = {226-236},
doi = {10.1093/bioinformatics/17.3.226},
url = {},

Home : Publications : Report 

Please mail <> with any changes or corrections.
Unless explicitly stated otherwise, all material is copyright The University of Edinburgh