Combinatorial approaches to gene recognition*

Computers and Chemistry

Volumn 21, Issue 4, 1997, Pages 229-235

  Roytberg, M A ^a   Astakhova, T V ^a   Gelfand, M S ^b  

^a INSTITUTE OF MATHEMATICAL PROBLEMS OF BIOLOGY   (Russian Federation)

^b INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PRIMER DNA;

ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; EXON; GENETIC PROCEDURES; GENETICS; MATHEMATICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION;

BASE SEQUENCE; DNA; DNA PRIMERS; EXONS; GENETIC TECHNIQUES; MATHEMATICS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE PROBES; POLYMERASE CHAIN REACTION; READING FRAMES; SOFTWARE;

EID: 0031299666     PISSN: 00978485     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0097-8485(96)00034-4     Document Type: Article

References (23)

1. Aho, A., Hopcroft, J. and Ullman, J. (1976) The Design and Analysis of Computer Algorithms. Addison-Wesley, Reading, MA.
2. Brodsky, L. I., Drachev, A. L., Leontovich, A. M. and Feranchuk, S. I. (1993) A novel method of multiple alignment of biopolymer sequences. BioSystems 30, 65-79.
3. Burset, M. and Guigo, R. (1996) Evaluation of gene structure prediction programs. Genomics 34, 353-375.
4. D'Esposito, M., Mazzarells, R., Pengue, G., Jones, C., D'Urso, M. and Schlessinger, D. (1994) PCR-cased immortalization and screening of heirarchial pools of cDNAs. Nucleic Acids Research 22, 4806-4809.
5. Fickett, J. W. and Tung, C.-S. (1992) Assessment of protein coding measure Nucleic Acids Research 20, 6441-6450.
6. Finkelstein, A. V. and Roytberg, M. A. (1993) Computation of biopolymers: a general approach to different problems. BioSystems 30, 1-19.
7. Gelfand, M. S. (1989) Statistical analysis of mammalian pre-mRNA splicing sites. Nucleic Acids Research 17, 6369-6382.
8. Gelfand, M. S. (1990) Computer prediction of the exon-intron structure of mammalian pre-mRNAs. Nucleic Acids Research 18, 5865-5869.
9. Gelfand, M. S. (1995) Prediction of function in DNA sequence analysis. Journal of Computational Biology 2, 87-115.
10. Gelfand, M. S. and Roytberg, M. A. (1993) Prediction of the exon-intron structure by a dynamic programming approach. BioSystems 30, 173-182.
11. Gelfand, M. S., Podolsky, L. I., Astakhova, T. V. and Roytberg, M. A. (1996a) Recognition of genes in human DNA sequences. Journal of Computational Biology 3, 223-234.
12. Gelfand, M. S., Mironov, A. A. and Pevzner, P. A. (1996b) Gene recognition via spliced sequence alignment Proceedings of the National Academy of Sciences of the U.S.A. 93, 9061-9066.
13. Korning, P. G., Hebsgaard, S. M., Rouze, P. and Brunak, S. (1996) Cleaning the GenBank Arabidopsis thaliana data set. Nucleic Acids Research 24, 316-320.
14. Parrich, J. E. and Nelson, D. L. (1993) Methods for finding genes: a major rate-limiting step in positional cloning. Gene. Analysis Techniques and Applications 10, 29-41.
15. Piterbarg, V. I. (1992) On the Distribution of the maximum similarity score for fragments of two random sequences. In DIMACS Series on Discrete Mathematics and Theoretical Computer Science, ed. S. Gindikin, Vol. 8, pp. 11-18. AMS, Providence, RI.
16. Roytberg, M. A., Astakhova, T. V. and Gelfand, M. S. (1996) An algorithm for highly specific recognition of protein coding regions. In Genome Informatics 1996, Proceedings of the 7th Workshop on Genome Informatics, Tokyo, December 1996, pp. 82-87.
17. Roytberg, M. A., Astakhova, T. V. and Gelfand, M. S. (1997) Algorithm for highly specific recognition of protein coding regions in DNA sequences of higher eukaryotes (in Russian). Molekulyarnaya Biologiya 31, 25-31.
18. Sharp, P. A. (1994) Split genes and RNA splicing. Cell 77, 805-815.
19. Snyder, E. E. and Stormo, G. D. (1993) Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks. Nucleic Acids Research 21, 607-613.
20. Snyder, E. E. and Stormo, G. D. (1995) Identification of protein coding regions in genomic DNA. Journal of Molecular Biology 248, 1-18.
21. Stormo, G. D. and Haussler, D. (1994) Optimally parsing a sequence into different classes based on multiple types of evidence. In Proceedings of the 2nd International Conference on Intelligent Systems for Molecular Biology, eds R. Altman, D. Brutlag, P. Karp, R. Lathrop and D. Searls, pp. 369-375. AAAI Press, Menlo Park, CA.
22. Xu, Y., Mural, R. J., Shah, M. and Uberbacher, E. C. (1994a) Recognizing exons in genomic sequence using GRAIL II. In Genetic Engineering: Principles and Methods, ed. J. Setlow, Vol. 16, pp. 241-253. Plenum Press, New York.
23. Xu, Y., Mural, R. J. and Uberbacher, E. C. (1994b) Constructing gene models from accurately predicted exons: an application of dynamic programming. Computer Applications in the Biosciences 10, 613-623.