Regular biosequence pattern matching with cellular automata

Authors:
Kim Laurio;Fredrik Linåker;Ajit Narayanan
Affiliations:
Department of Computer Science, Uníversity of Skövde, Box 408, 541 28 Skóvde, Sweden and Department of Computer Science, University of Exeter, EX4 4QF, UK;Department of Computer Science, Uníversity of Skövde, Box 408, 541 28 Skóvde, Sweden and Department of Computer Science University of Sheffield, S1 4DP, UK;Department of Computer Science, Uníversity of Skövde, Box 408, 541 28 Skóvde, Sweden and Department of Computer Science, University of Exeter, EX4 4QF, UK
Venue:
Information Sciences—Applications: An International Journal
Year:
2002

Citing 9
Cited 4

Parallel language recognition in constant time by cellular automata.

Acta Informatica
Compilers: their design and construction using Pascal

Compilers: their design and construction using Pascal
Compilers: principles, techniques, and tools

Compilers: principles, techniques, and tools
A scalable systolic multiprocessor system for analysis of biological sequences

Proceedings of the 1993 symposium on Research on integrated systems
Text algorithms

Text algorithms
An implementation of von Neumann's self-reproducing machine

Artificial Life
Parallel Computation in Biological Sequence Analysis

IEEE Transactions on Parallel and Distributed Systems
Quasi-Uniform Computation-Universal Cellular Automata

Proceedings of the Third European Conference on Advances in Artificial Life
A Bit-Parallel Approach to Suffix Automata: Fast Extended String Matching

CPM '98 Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching

Non-uniform cellular automata based associative memory: Evolutionary design and basins of attraction

Information Sciences: an International Journal
Analysis of DNA sequence transformations on grids

Journal of Parallel and Distributed Computing
On behavior of two-dimensional cellular automata with an exceptional rule

Information Sciences: an International Journal
Fluctuation-driven computing on number-conserving cellular automata

Information Sciences: an International Journal

Quantified Score

Hi-index	0.00

Visualization

Abstract

Could algorithms designed within the computational model of cellular automata fit well into a future biocomputing environment where data and computation are seamlessly and dynamically distributed? We suggest it is possible by presenting a systematic approach for creating 1D linear cellular automata that in parallel can locate all starting positions of complete matches to a given PROSITE pattern in a string. The cellular automaton requires time proportional to the maximal length of a pattern match, and is inherently suited for distribution out on multiple processors.