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Speeding up parsing of biological context-free grammars

Fredouille, D and Bryant, CH 2005, 'Speeding up parsing of biological context-free grammars' , in: Proceedings of the 16th Annual Symposium on Combinatorial pattern matching , Lecture notes in computer science (3537) , Springer, Berlin / Heidelberg, Germany, pp. 241-256.

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Abstract

Grammars have been shown to be a very useful way to model biological sequences families. As both the quantity of biological sequences and the complexity of the biological grammars increase, generic and efficient methods for parsing are needed. We consider two parsers for context-free grammars: depth-first top-down parser and chart parser; we analyse and compare them, both theoretically and empirically, with respect to biological data. The theoretical comparison is based on a common feature of biological grammars: the gap - a gap is an element of the grammars designed to match any subsequence of the parsed string. The empirical comparison is based on grammars and sequences used by the bioinformatics community. Our conclusions are that: (1) the chart parsing algorithm is significantly faster than the depth-first top-down a lgorithm, (2) designing special treatments in the algorithms for managing gaps is useful, and (3) the way the grammar encodes gaps has to be carefully chosen, when using parsers not optimised for managing gaps, to prevent important increases in running times.

Item Type: Book Section
Editors: Apostolico, A, Crochemore, M and Park, K
Additional Information: Paper originally presented at the 16th Annual Symposium, CPM 2005, Jeju Island, Korea, June 19-22 2005
Themes: Subjects / Themes > Q Science > QA Mathematics > QA075 Electronic computers. Computer science
Subjects / Themes > Q Science > QH Natural history > QH301 Biology
Subjects outside of the University Themes
Schools: Colleges and Schools > College of Science & Technology
Colleges and Schools > College of Science & Technology > School of Computing, Science and Engineering
Colleges and Schools > College of Science & Technology > School of Computing, Science and Engineering > Data Mining and Pattern Recognition Research Centre
Publisher: Springer
Refereed: Yes
Series Name: Lecture notes in computer science
ISBN: 9783540262015
Related URLs:
Depositing User: Dr Chris H. Bryant
Date Deposited: 16 Feb 2009 14:16
Last Modified: 20 Aug 2013 15:55
URI: http://usir.salford.ac.uk/id/eprint/1758

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