Homology-based gene prediction using neural nets

Analytical Biochemistry

Volumn 265, Issue 2, 1998, Pages 269-274

  Cai, Yudong ^a,b   Bork, Peer ^a,b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

Gene prediction; Homology searches; Neural nets

Indexed keywords

FORECASTING; HEMOGLOBIN; NEURAL NETWORKS; PROTEINS;

EXPRESSED SEQUENCE TAG DATABASE; GENE IDENTIFICATION; GENE PREDICTION; HOMOLOGY INFORMATION; HOMOLOGY SEARCH; NON-CODING REGION; OVERALL ACCURACIES; SCORING FUNCTIONS;

GENES;

DNA; GLOBIN; PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; GENE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN DETERMINATION; SEQUENCE HOMOLOGY;

VERTEBRATA;

EID: 0032534796     PISSN: 00032697     EISSN: None     Source Type: Journal    
DOI: 10.1006/abio.1998.2876     Document Type: Article

References (24)

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. J. Mol. Biol. 215:1990;403-410.
2. Bork P., Bairoch A. Trends Genet. 12:1996;425-427.
3. Bork P., Ouzounis C., Sander C. From genome sequences to protein function. Curr. Opin. Struct. Biol. 4:1994;393-403.
4. Borodovsky M., McIninch J. Comp. Chem. 17:1993;123-134.
5. Burge C., Karlin S. J. Mol. Biol. 268:1997;78-94.
6. Burset M., Guigo R. Genomics. 34:1996;353-367.
7. Dong S., Searls D. B. Genomics. 23:1994;540-551.
8. Fitch D., Bailey W., Tagle D., Goodman M., Sieu L., Slightom J. Proc. Natl. Acad. Sci. USA. 88:1991;7396-7400.
9. Gelfand M. S., Mironov A. A., Pevzner P. A. Proc. Natl. Acad. Sci. USA. 93:1996;9061-9066.
10. Gish W., States D. J. Nature Genet. 3:1993;266-272.
11. Guigo R., Knudsen S., Drake N., Smith T. J. Mol. Biol. 226:1992;141-157.
12. Henderson J., Salzberg S., Fasman K. J. Comp. Biol. 4:1997;119-126.
13. Hutchinson G. B., Hayden M. R. Nucleic Acids Res. 20:1992;3453-3462.
14. Jurka, J. 1995, Database of Repetitive Elements (Repbase), ftp://ncbi.nlm.nih.gov/repository/repbase/.
15. Kulp, D. Haussler, D. Reese, M. G. Eeckman, F. H. 1996, A Generalized Hidden Markov Model for the Recognition of Human genes in DNA, AAAI Press, Menlo Park, CA.
16. Rogozin I., Milanesi L., Kolchanov A. Comp. Appl. Biol. Sci. 12:1996;161-170.
17. Salzberg, S. Delcher, A. Fasman, K. Henderson, J. 1997, A Decision Tree System for Finding Genes in DNA, Department of Computer Science, Johns Hopkins University.
18. Solovyev V. V., Salamov A. A., Lawrence C. B. Nucleic Acids Res. 22:1994;5156-5163.
19. Snyder E. E., Stormo G. D. J. Mol. Biol. 248:1995;1-18.
20. Warren P., Sally A. Mol. Microbiol. 21:1996;213-219.
21. Werbos, P. 1974, Beyond Regression: New Tools for Prediction and Analysis in Behavioral Sciences, Appl. Math. Harvard University, Cambridge, MA.
22. Wootton J., Federhen S. Comp. Chem. 17:1993;149-163.
23. Xu, Y. Einstein, J. R. Mural, R. J. Shah, M. Uberbacher, E. C. 1994, An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequences, 376, 383, AAAI Press, Menlo Park, CA.
24. Zhang M. Q. Proc. Natl. Acad. Sci. USA. 94:1997;559-564.