原创力文档a stochastic context free grammar based framework for analysis of protein sequences基于随机上下文无关语法的框架分析的蛋白质序列.pdfVIP
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a stochastic context free grammar based framework for analysis of protein sequences基于随机上下文无关语法的框架分析的蛋白质序列
BMC Bioinformatics BioMed Central
Research article Open Access
A stochastic context free grammar based framework for analysis of
protein sequences
Witold Dyrka†1 and Jean-Christophe Nebel*†2
Address: 1Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Poland and 2Faculty of Computing,
Information Systems Mathematics, Kingston University, London, UK
Email: Witold Dyrka - Witold.Dyrka@pwr.wroc.pl; Jean-Christophe Nebel* - J.Nebel@kingston.ac.uk
* Corresponding author †Equal contributors
Published: 8 October 2009 Received: 17 December 2008
Accepted: 8 October 2009
BMC Bioinformatics 2009, 10:323 doi:10.1186/1471-2105-10-323
This article is available from: /1471-2105/10/323
© 2009 Dyrka and Nebel; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background: In the last decade, there have been many applications of formal language theory in
bioinformatics such as RNA structure prediction and detection of patterns in DNA. However, in
the field of proteomics, the size of the protein alphabet and the complexity of relationship between
amino acids have mainly limited the application of formal language theory to the production of
grammars whose expressive power is not higher than stochastic regular grammars. However, these
grammars, like o
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