The Gene-Finder computer tools for analysis of human and model organisms genome sequences

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, ISMB 1997

Volumn , Issue , 1997, Pages 294-302

  Solovyev, Victor ^a   Salamov, Asaf ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; CODES (SYMBOLS); DNA SEQUENCES; DYNAMIC PROGRAMMING; GENE ENCODING; PATTERN RECOGNITION; WEBSITES;

COMPUTER TOOLS; GENE STRUCTURE; GENOME SEQUENCES; GENOMIC DNA; HUMAN GENES; HUMAN ORGANISMS; MODEL ORGANISMS; NEW PROJECTS; SPLICE SITE; STRUCTURE IDENTIFICATION;

FORECASTING;

DNA;

ANIMAL; ARTICLE; BACTERIAL GENE; BIOLOGICAL MODEL; COMPUTER PROGRAM; EXON; FACTUAL DATABASE; GENETICS; GENOME; HUMAN; METHODOLOGY; PROMOTER REGION; RNA SPLICING; SEQUENCE ALIGNMENT; STATISTICS;

ANIMALS; DATABASES, FACTUAL; DNA; EXONS; GENES, BACTERIAL; GENOME; GENOME, HUMAN; HUMANS; MODELS, GENETIC; PROMOTER REGIONS (GENETICS); RNA SPLICING; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 0030627562     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (38)

1. Aebi M., Weissmann C. (1987) Precision and orderliness in splicing.Trends in Genetics, 3,102-107.
2. Breathnach R.,Chainbon P. (1981) Organization and expression of eukaryotic split genes for coding proteins. Ann.Rev.Biochem., 50,349-393.
3. Berg, O.G., von ffippel, P.H. (1987). Selection of DNA binding sites by regulatory proteins. J.Mol.Biol., 193, 723-750.
4. Burset M., Guigo R. (1996), Evaluation of gene structure prediction programs, Genomics, 34(3), 353-367.
5. Gormen T.H., Leiserson C.E., Rivest R.L. 1990. Introduction to Algorithms. MIT Press.
6. Decker C.J. and Parker R. (1995) Diversity of cytopasmatic functions for the 3'-untranslated region of eukaryotic transcripts. Current Opinions in Cell Biology 1995,7: 386-392.
7. Dong S., Scarls D.(1994), Gene structure prediction by linguistic methods. Genomics, 23, 540-551.
8. Brunak, S.; Engelbreht J.; Knudsen S. (1991) Prediction of Human mRNA donor and acceptor sites from the DNA sequence. J. Mol Biol. 220:49-65.
9. Efron B., Tibshirani R. (1991) Statistical data analysis in the computer age. Science, 253,390-395.
10. Fickett J.W.; Tung CS. 1992. Assessment of Protein Coding Measures. Nucl. Acids Res. 20: 6441-6450.
11. Fields CSoderlund C. (1990) GM: a practical tool for automating DNA sequence analysis", CABIOS, 6, 263-270.
12. Gelfand M. (1989) Statistical analysis of mammalian pre-mRNA splicing sites, Nucleic Acids Research, 17, 6369-6382.
13. Gelfand M. (1990), Global methods for the computer prediction of protein-coding regions in nucleotide sequences. Biotechnology Software, 7, 3-11.
14. Gelfand M.,Roytberg M. (1993), Prediction of the exon-intron structure by a dynamic programming approach, BioSystems, 30(1-3), 173-182.
15. Ghosh, D. (1993). Status of the transcription factors database (TFD). Nuci. Acids Res.21, 3117-3118.
16. Green M.R. (1991) Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. Ann.Rev.Ce1I Biol.,7,559-599.
17. Guigo R.; Knudsen S.; Drake N.;Smith T.(1992) Prediction of gene structure.J.Mol.Biol.226:141-157.
18. Hutchinson G.B., Hayden M.R. 1992. The prediction of exons through an analysis of splicible open reading frames. Nucl.Acids Res. 20:3453-3462.
19. Hebsgaard S., Koming R, Tolstrup N., Engelbrecht J., Rouze R, Brunak S. (1966) Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucl.Acids Res., 24,3439-3452.
20. Kondrakhin Y, Shamin V., Kolchanov N. (1994) Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3'-termina] processing sites. Comput. Applic. Biosci., 10, 597-603.
21. Kulp D., Haussler D., Reese M., Eeckman E(1996) A generalized hidden Markov model for the recognition of human genes in DNA, in In Proceedings of the 4th International Conference on Intelligent Systems for Molecular Biology, 134-142.
22. Lapedes A.; Barnes C; Burks C; Färber R.;Sirotkin K. (1988) Application of neural network and other machine learning algorithms to DNA sequence analysis. In Proceedings Santa Fc Institute 7: 157-182.
23. Mount S.M. (1982) A catalogue of splice junction sequences. Nucl.Acids Res. 10: 459-472.
24. Mount S.M. (1993) Messenger RNA splicing signal in Drosophila genes. In An atlas of Drosophila genes (ed. Maroni G.), Oxford.
25. Nakata K.; Kanehisa M.; DeLisi C. (1985) Prediction of splice junctions in mRNA sequences. Nucl.Acids Res. 13: 5327-5340.
26. Prestridge D.S. (1995) Predicting Pol U promoter sequences using transcription factor binding sites. J. Mol. Biol, 249: 923-932.
27. Senapathy F; Shapiro M.B.; Harris N.L.(1990) Splice junctions. Branch point sites, and Exons. Methods of Enzymology (ed. R.F. Doolittle) 183: 252-280.
28. Snyder E.E.,Stormo G.D. (1993) Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks. Nucl.Acids Res., 21:607-613.
29. Salamov A.A., Solovyev V.V. (1997) Recognition of 3'-processing sites of human mRNA precursors. CABIOS 13, 23-28.
30. Solovyev V.V., Lawrence C.B. (1993) Identification of Human gene functional regions based on oligonucleotide composition. In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology (eds. Hunter L.,Searls D.,Shavlik J.), p.371-379.
31. Solovyev, V., Lawrence, C. (1993b) Prediction of human gene structure using dynamic programming and oligonucleotide composition In: Abstracts of the 4th annual Keck symposium. Pittsburgh, 47.
32. Solovyev V.V., Salamov A.A., Lawrence C.B. (1994) Predicting internal exons by oligonucleotide composition and discriminant analysis of splicible open reading frames. Nucleic Acids Res. 22,N 24, 5156-5163.
33. Solovyev V.V., Salamov A.A., Lawrence C.B. (1995) Prediction of human gene structure using linear discriminant functions and dynamic programming. In Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (eds. Rawling CClark D.,Altman R.,Hunter L.,Lengauer T.,Wodak S.), Cambridge,England, AAAI Press,367-375.
34. Uberbacher E.C., Xu Y, Mural R.J. (1996) Discovering and understanding genes in Human DNA sequences using GRAIL, in Methods Enzimology (ed. Doolittle R.), 266, 259-281.
35. Wingender, E. (1994) Recognition of regulatory regions in genomic sequences. J.Biotechnol. 35, 273-280.
36. Xu Y, J.R. Einstein, R.J. Mural, M. Shah and E.C. Uberbacher (1994) An improved system for exon recognition and gene modeling in human DNA sequences". In Proceedings of the 2nd International Conference on Intelligent Systems for Molecular Biology (eds. Altman R., Brutlag, Karp P, Lathrop R. and Searls D.) 376-383.
37. Xu Y, Uberbacher E. (1996) Gene prediction by pattern recognition and homology search. In Proceedings of the 4th International Conference on Intelligent Systems for Molecular Biology, 241-252.
38. Yada T., Ishikava M., Totoki Y, Okubo K. (1994) Statistical analysis of Human DNA sequences in the vicinity of poly-A signal. In Proceedings of the 2-nd International conference on Bioinformatics, Supercomputing, and Complex genome analysis.