Chapter 7 Computational gene prediction using neural networks and similarity search

New Comprehensive Biochemistry

Volumn 32, Issue C, 1998, Pages 109-128

  Xu, Ying ^a   Uberbacher, EdwardC ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77956699406     PISSN: 01677306     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0167-7306(08)60464-0     Document Type: Chapter

References (26)

1. Fickett J.W. Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 10 (1982) 5303-5318
2. Borodovsky M., Sprizhitskii Yu., Golovanov E., and Aleksandov A. Statistical patterns in the primary structures of functional regions in E. coli. Mol. Biol. 20 (1986) 1390-1398
3. Gelfand M.S. Computer prediction of exon-intron structure of mammalian pre-mRNAs. Nucleic Acids Res. 18 (1990) 5865-5869
4. Uberbacher E.C., and Mural R.J. Locating protein-coding regions in human DNA sequences by a multiple sensors-neural network approach. Proc. Natl. Acad. Sci. USA 88 (1991) 11261-11265
5. Guigo R., Knudsen S., Drake N., and Smith T. Prediction of gene structure. J. Mol. Biol. 226 (1992) 141-157
6. Hutchinson G.B., and Hayden M.R. The prediction of exons through an analysis of spliceable open reading frames. Nucleic Acids Res. 20 (1992) 3453-3462
7. Snyder E.E., and Stormo G.D. Identification of coding regions in genomic DNA sequences: An application of dynamic programming and neural networks. Nucleic Acids Res. 21 (1993) 607-613
8. Xu Y., Mural R.J., and Uberbacher E.C. Constructing gene models from a set of accurately-predicted exons: An application of dynamic programming. Comput. Appl. Biosci. 10 (1994) 613-623
9. Dong S., and Searls D.B. Gene structure prediction by linguistic methods. Genomics 23 (1994) 540-551
10. Solovyev V.V., Salamov A.A., and Lawrence C.B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res. 22 (1994) 5156-5163
11. Kulp D., Haussler D., Reese M.G., and Eckerman F.H. In: States D.J., Agarwal P., Gaasterland T., Hunter L., and Smith R. (Eds). A generalized hidden Markov model for the representation of human genes in DNA (1996), AAAI Press, Menlo Park, CA 134-142 Proc. 4th Int. Conf. on Intelligent Systems for Molecular Biology
12. Gelfand M., Mironov A., and Pevzner P. Gene recognition via spliced alignment. Proc. Natl. Acad. Sci. USA 93 (1996) 9061-9066
13. Salzberg S., Chen X., Henderson J., and Fasman K. Finding genes in DNA using decision trees and dynamic programming (1996), AAAI Press, Menlo Park, CA 201-210 Proc. 4th Int. Conf. on Intelligent Systems for Molecular Biology
14. Uberbacher E.C., Xu Y., and Mural R.J. Discovering and understanding genes in human DNA sequence using GRAIL. Methods Enzymol. 266 (1996) 259-281
15. Claverie J.M., Sauvaget I., and Bougueleret L. k-tuple frequency analysis: from intron/exon discrimination to T-cell epitope mapping. Methods Enzymol. 183 (1990) 237-252
16. Xu Y., and Uberbacher E.C. Automated gene structure identification in large-scale genomic sequences. J. Comp. Biol. 4 3 (1997) 325-338
17. Costanzo F., Castagnoli L., Dente L., Arcari P., Smith M., Costanzo P., Raugel G., Izzo P., Pietronaolo T.C., Bougueleret L., Cimino E., Salvatore F., and Cortese R. Cloning of several cDNA segments coding for human liver proteins. EMBO J. 2 (1983) 57-61
18. Adams M.D., Kelley J.M., Gocayne J.D., Dubnick M., Polymeropolous M.H., Xiao H., Merril C.R., Wu A., Olde B., Moreno R.F., Kerlavage A.R., McCombie W.R., and Venter J.C. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252 (1991) 1651-1656
19. Wilcox A.S., Khan A.S., Hopkins J.A., and Sikela J.M. Use of 3′ untranslated sequences of human cDNAs for rapid chromosome assignment and conversion to STSs: implications for an expression map of the genome. Nucleic Acids Res. 19 (1991) 1837-1843
20. Houlgatte R., Mairage-Samson R., Duprat S., Tessier A., Bentolila S., Lamy B., and Auffray C. The gene-express index: A resource for gene discovery and the genic map of the human genome. Genome Res. 5 (1995) 272-304
21. Adams M.D., et al. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377 (1995) 3-174
22. Aaronson J.S., Eckman B., Blevins R.A., Borkowski J.A., Myerson J., Imran S., and Elliston K.O. Towards the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data. Genome Res. 6 (1996) 829-845
23. Hertz J., Krogh A., and Palmers A.R.G. Introduction to The Theory of Neural Computation (1991), Addison-Wesley, Reading, MA
24. Xu Y., Mural R.J., and Uberbacher E.C. An iterative algorithm for correcting sequencing errors in DNA coding regions. J. Comp. Biol. 3 (1996) 333-344
25. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tools. J. Mol. Biol. 215 (1990) 403-410
26. Boguski M.S., Lowe T.M., and Tolstoshev C.M. dbEST - database for expressed sequence tags. Nat. Genet. 4 (1993) 332-333