Regular biosequence pattern matching with cellular automata

Information Sciences

Volumn 146, Issue 1-4, 2002, Pages 89-101

  Laurio, Kim ^a,b   Linåker, Fredrik ^a,c   Narayanan, Ajit ^a,b  

^a UNIVERSITY OF SKÖVDE   (Sweden)

^b UNIVERSITY OF EXETER   (United Kingdom)

^c UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

Biosequence; Cellular automata; Pattern matching; Regular expression

Indexed keywords

ALGORITHMS; CELLS; COMPUTATION THEORY; MATHEMATICAL MODELS; MOLECULAR BIOLOGY;

CELLULAR AUTOMATA;

PATTERN MATCHING;

EID: 0036800403     PISSN: 00200255     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0020-0255(02)00303-1     Document Type: Article

References (24)

1. Aho A., Sethi R., Ullman J. Compilers - Principles, Techniques and Tools. 1986;Addison-Wesley.
2. A. Bairoch, PROSITE: a dictionary of protein sites and patterns - user manual. Release 16 July 1999. (online), Swiss Institute of Bioinformatics, Geneva, Switzerland, (Available from http://www.expasy.ch/prosite/) (Accessed 29 September 2001).
3. Berlekamp E., Conway J.H., Guy R. Winning Ways for Your Mathematical Plays. vol. 2:1982;Academic Press.
4. Bussemaker H.J., Li H., Siggia E. Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis. Proc. Natl. Acad. Sci., USA. 97(18):2000;10096-10100.
5. Branden C., Tooze J. Introduction to Protein Structure. 1991;Garland Publishing.
6. Cole S.N. Real-time computation by n-dimensional iterative arrays of finite-state machines. IEEE Trans. Comput. C-18(4):1969;349-365.
7. Crochemore M., Rytter W. Text Algorithms. 1994;Oxford University Press.
8. M. Delorme, J. Mazoyer, Cellular Automata as Language Recognizers, Laboratoire de l'Informatique du Parallélisme, Research Report 98-36, 1998
9. L. Gong, Project JXTA: a technology overview. (online), Sun Microsystems, Palo Alto, USA, 2001 (Available from http://www.jxta.org/) (Accessed 29 September 2001).
10. Grundy W.N., Bailey T.L., Elkan C.P. ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. CABIOS. 12:1996;303-310.
11. Hunter R. Compilers - Their Design and Construction Using Pascal. 1985;John Wiley and Sons.
12. Hofman K., Bucher P., Falquet L., Bairoch A. The PROSITE database, its status in 1999. Nucl. Acids Res. 27(1):1999;215-219.
13. Kung H.T. Why systolic architectures? Computer. 15(1):1982;37-46.
14. M. Mitchell, Computation in cellular automata: a selected review, Santa Fe Institute, Working Paper 9609-074, 1996
15. Navarro G., Raffinot M. A bit-parallel approach to suffix automata: fast extended string matching. Farach-Colton M. Proc. of the 9th Annual Symposium on Combinatorial Pattern Matching. 1998;14-33 Springer-Verlag.
16. Pesavento U. An implementation of von Neumann's self-reproducing machine. Artificial Life J. 2(4):1996;337-354.
17. Rognes T., Seeberg E. Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics. 16(8):2000;699-706.
18. Seiferas J.I. Linear-time computation by nondeterministic multidimensional iterative arrays. SIAM J. Comput. 6(3):1977;487-504.
19. Singh R.K., Tell S.G., White C.T., Hoffman D., Chi V.L., Erickson B.W. A scalable systolic multiprocessor for analysis of biological sequences. Proc. Symp. on Integrated Systems. 1993;168-182 MIT-Press.
20. Sipper M. Quasi-uniform computation-universal automata. Moránet al. Proc. of the 3rd European Conference on Artificial Life (ECAL'95). 1995;544-554 Springer-Verlag.
21. Smith A.R. Real-time language recognition by 1D cellular automata. J. Comput. Syst. Sci. 6:1972;233-253.
22. Sommerhalder R., van Westrhenen S.C. Parallel language recognition in constant time by cellular automata. Acta Informat. 19:1983;397-407.
23. Terrier V. Language recognizable in real time by cellular automata. Complex Syst. 8:1994;325-336.
24. Yap T.K., Frieder O., Martino R.L. Parallel computation in biological sequence analysis. IEEE Trans. Parallel Distr. Syst. 9(3):1998.