A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA

Proceedings of the 4th International Conference on Intelligent Systems for Molecular Biology, ISMB 1996

Volumn , Issue , 1996, Pages 134-142

  Kulp, David ^a   Haussler, David ^a   Reese, Martin G ^b   Eeckman, Frank H ^b  

^a University of California Santa Cruz   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMIC PROGRAMMING; GENES; HIDDEN MARKOV MODELS; LEARNING SYSTEMS; NUCLEOTIDES;

CANDIDATE SEQUENCES; DYNAMIC PROGRAMMING ALGORITHM; GENE FINDING; GENERALIZED HIDDEN MARKOV MODELS; HIDDEN-MARKOV MODELS; HUMAN GENES; MACHINE LEARNING TECHNIQUES; NUCLEOTIDE BASIS; STATISTIC MODELING; TRAINING SETS;

DNA;

DNA;

ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; EXON; GENE DELETION; HUMAN; HUMAN CHROMOSOME; INTRON; PROBABILITY;

CHROMOSOMES, HUMAN; DNA; EXONS; HUMANS; INTRONS; MARKOV CHAINS; MODELS, GENETIC; SEQUENCE DELETION; SOFTWARE;

EID: 0030333286     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (23)

1. Auger, I. E ., and Lawrence, C. E. 1989. Algorithms for the optimal identification of segment neighborhoods. 5«//. Math. Biol. 51:39-54.
2. Bengio, Y . 1996. Neural Networks for Speech and Sequence Recognition. Thomson.
3. Borodovsky, M., and Mclninch, J. 1993. Genmark: Parallel gene recognition for both DNA strands. Computers and Chemistry 17(2):123-133.
4. Brunak, S.; Engelbrecht, J .; and Knudsen, S. 1991. Prediction of human mRNA donor and acceptor sites from the dna sequence. J M B 220:49-65.
5. Burset, M., and Guigo, R. 1996. Evaluation of gene structure prediction programs. Genomics (to appear). Data set and evaluation results can be found at http://www.imim.es/GeneIdentification/Evaluation/Index.html.
6. Dong, S., and Searls, D. B. 1994. Gene structure prediction by linguistic methods. Genomics 162:705¬ 708.
7. Fickett, J. W., and Tung, C.-S. 1992. Assessment of protein coding measures. Nucl. Acids Res. 20:6441¬ 6450.
8. Fong, D. 1995. Parsing of DNA sequences using dynamic programming with a state machine model, unpublished manuscript.
9. Gelfand, M. S., and Roytberg, M. A. 1993. Prediction of the exon-intron structure by a dynamic programming approach. BioSysiems 30:173-182.
10. Gelfand, M. S., and Roytberg, M. A. 1995. Dynamic programming for gene recognition. In Gene-Finding and Gene Structure Prediction Workshop.
11. Guigo, R.; Knudsen, S.; Drake, N.; and Smith, T. 1992. Prediction of gene structure. J. Mol. Biol. 226:141-157.
12. Hawkins, J. D. 1988. A survey on intron and exon lengths. Nucl. Acids Res. 16:9893-9908.
13. Krogh, A.; Brown, M.; Mian, I. S.; Sjölander, K .; and Haussler, D. 1994. Hidden Markov models in computational biology: Applications to protein modeling. JMB 235:1501-1531.
14. Krogh, A.; Mian, I. S.; and Haussler, D. 1994. A Hidden Markov Model that finds genes in E . coli DNA. NAR 22:4768-4778.
15. Rabiner, L. R., and Juang, B. H. 1986. An introduction to hidden Markov models. I E E E ASSP Magazine 3(1):4-16.
16. Reese, M. G. 1995. Novel neural network prediction systems for human promoters and splice sites. In Gene-Finding and Gene Structure Prediction Workshop.
17. Sankofl", D. 1992. Efficient optimal decomposition of a sequence into disjoint regions, each matched to some template in an inventory. Math. Biosci. 111:279-293.
18. Smith, M. W. 1988. Structure of vertebrate genes: a statistical analysis implicating selection. J. Mol. Evol. 27:45-55.
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. Nud. Acids Res. 21:607-613.
20. Solovyev, V.; A., S.; and Lawrence, C. 1994. Predicting internal exons by oligonucleotide composition and discriminant analysis of splicable open reading frames. Nuci Acids Res. 22:5156-5163.
21. Stormo, G. D., and Haussler, D. 1994. Optimally parsing a sequence into different classes based on multiple types of information. In ISMB-94- Menlo Park, C A: A A A I / M I T Press.
22. Wu, T. 1995. A phase-specific dynamic programming algorithm for parsing gene structure. In Gene-Finding and Gene Structure Prediction Workshop.
23. Xu, Y .; Einstein, J. R.; Shah, M.; and Uberbacher, E. C. 1994. An improved system for exon recognition and gene modeling in human dna sequences. In ISMB-94. Menlo Park, CA: A A A I / M I T Press.