Predictive methods using nucleotide sequences

Methods of Biochemical Analysis

Volumn 39, Issue , 1998, Pages 231-245

  Fickett, James W ^a  

^a GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSFER RNA;

ARTICLE; BIOLOGY; CODON; COMPUTER NETWORK; COMPUTER PROGRAM; DNA SEQUENCE; FACTUAL DATABASE; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; STATISTICS;

BASE SEQUENCE; CODON; COMPUTATIONAL BIOLOGY; COMPUTER COMMUNICATION NETWORKS; DATABASES, FACTUAL; DNA; MOLECULAR SEQUENCE DATA; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 0031633362     PISSN: 00766941     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (56)

1. Aaronson, J., Eckman, B., Blevins, R. A., Borkowski, J. A., Myerson, J., Imran, S., and Elliston, K. O. (1996). Toward the development of a gene index to the human genome: An assessment of the nature of high-throughput EST sequence data. Genome Res. 6, 829-845.
2. Barrick, D., Villaneuba, K., Childs, J., Kalil, R., Schneider, T. D., Lawrence, C. E., Gold, L., and Stormo, D. (1994). Quantitative analysis of ribosome binding sites in E. coli. Nucl. Acids Res. 22, 1287-1295.
3. Bork, P. (1996). Go hunting in sequence databases but watch out for the traps. Trends Genet. 12, 425-427.
4. Borodovsky, M., and McIninch, J. (1993). Genmark: Parallel gene recognition for both DNA strands. Compu. Chem. 17, 123-134.
5. Breiman, L., Friedman, J. H., Olshen, R. A., and Stone, C. J. (1984). Classification and Regression Trees (Pacific Grove, CA: Wadsworth and Brooks/Cole).
6. Brunak, S., Engelbrecht, J., and Knudsen, S. (1991). Prediction of human mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol. 220, 49-65.
7. Burge, C., and Karlin, S. (1997). Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94.
8. Burset, M., and Guigó, R. (1996). Evaluation of gene structure prediction programs. Genomics 34, 353-367.
9. Claverie, J.-M. (1996). Effective large-scale sequence similarity searches. Methods Enzymol. 266, 212-227.
10. Claverie, J.-M., and Sauvaget, I. (1985). Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters. Comput. Appl. Biosci. 1, 95-104.
11. Dalphin, M. E., Brown, C. M., Stockwell, P. A., and Tate, W. P. (1997). The translational signal database, TransTerm: More organisms, complete genomes. Nucl. Acids Res. 25, 246-247.
12. Dong, S., and Searls, D. B. (1994). Gene structure prediction by linguistic methods. Genomics 23, 540-551.
13. Doolittle, R. F. (1986). Of URFs and ORFs (Mill Valley, CA: University Science Books).
14. Duret, L., and Bucher, P. (1997). Searching for regulatory elements in human noncoding sequences. Curr. Opin. Struct. Biol. 7, 399-406.
15. Eddy, S. R., and Durbin, R. (1994). RNA sequence analysis using covariance models. Nucl. Acids Res. 22, 2079-2088.
16. Einstein, J. R., Mural, R. J., Guan, X., and Uberbacher, E. C. (1992). Computer-Based Construction of Gene Models Using the GRAIL Gene Assembly Program. Oak Ridge National Laboratory Report TM-12174 (Oak Ridge, TN-ORNL).
17. Fichant, G., and Burks, C. (1991). Identifying potential tRNA genes in genomic DNA sequences. J. Mol. Biol. 220, 659-671.
18. Fickett, J. W. (1996). Coordinate positioning of MEF2 and myogenin binding sites. Gene 172, GC19-GC32.
19. Fickett, J. W., and Guigó, R. (1996). Computational gene identification. In Internet for the Molecular Biologist, S. R. Swindell, R. R. Miller, and G. Myers, Eds. (Washington, DC: Horizon Scientific Press), pp. 73-100.
20. Fickett, J. W., and Hatzigeorgiou, A. G. (1997). Eukaryotic promoter recognition. Genome Res. 7, 861-878.
21. Fickett, J. W., and Tung, C.-S. (1992). Assessment of protein coding measures. Nucl. Acids Res. 20, 6441-6450.
22. Fondrat, C., and Kalogeropoulos, A. (1994). Approaching the function of new genes by the detection of their potential upstream activation sequences in Saccharomyces cerevisiae: Application to chromosome III. Curr. Genet. 25, 396-406.
23. Frech, K., Quandt, K., and Werner, T. (1997). Finding protein-binding sites in DNA sequences: The next generation. Trends Biochem. Sci. 22, 103-104.
24. Gelfand, M. S. (1995). Prediction of function in DNA sequence analysis. J. Comput. Biol. 2, 87-115.
25. Gelfand, M. S., Mironov, A. A., and Pevzner, P. A. (1996). Gene recognition via spliced alignment. Proc. Natl. Acad. Sci. U.S.A. 93, 9061-9066.
26. Gish, W., and States, D. J. (1993). Identification of protein coding regions by database similarity search. Nature Genet. 3, 266-272.
27. Green, P., Lipman, D., Hillier, L., Waterston, R., States, D., and Claverie, J.-M. (1993). Ancient conserved regions in new gene sequences and the protein databases. Science 259, 1711-1716.
28. Guigó, R. (1997). Computational gene identification. J. Mol. Med. 75, 389-393.
29. Guigó, R., Knudsen, S., Drake, N., and Smith, T. (1992). Prediction of gene structure. J. Mol. Biol. 226, 141-157.
30. Hillier, L., Lennon, G., Becker, M., Bonaldo, M. F., Chiapelli, B., Chissoe, S., Dietrich, N., DuBuque, T., Favello, A., Gish, W., Hawkins, M., Hultman, M., Kucaba, T., Lacy, M., Le, M., Le, N., Mardis, E., Moore, B., Morris, M., Parsons, J., Prange, C., Rifkin, L., Rohlfing, T., Schellenberg, K., Soares, M. B., Tan, F., Thierry-Meg, J., Trevaskis, E., Underwood, K., Wohldman, P., Waterston, R., Wilson, R., and Marra, M. (1996). Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6, 807-828.
31. Jurka, J., Klonowski, P., Dagman, V., and Pelton, P. (1996). CENSOR - A program for identification and elimination of repetitive elements from DNA sequences. Comput. Chem. 20, 119-122.
32. Knudsen, S., and Brunak, S. (1997). Kissing loops hide premature termination codons in pre-mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts. RNA 3, 697-701.
33. Kondrakhin, Y., Shamir, V., and Kolchanov, N. (1994). Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3′ terminal processing sites. Comput. Appl. Biosci. 10, 597-603.
34. Kozak, M. (1996) Interpreting cDNA sequences: Some insights from studies on translation. Mamm. Genome 7, 563-574.
35. Krogh, A., Mian, I. S., and Haussler, D. (1994). A hidden Markov model that finds genes in E. coli DNA. Nucl. Acids Res. 11, 4768-4778.
36. Kulp, D., Haussler, D., Reese, M. G., and Eckman, F. H. (1996). A generalized hidden Markov model for the recognition of human genes in DNA, In Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology, D. J. States, P. Agarwal, T. Gaasterland, L. Hunter, and R. Smith, Eds. (Menlo Park, CA: AAAI Press), pp. 134-142.
37. Lowe, T. M. and Eddy, S. R. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res. 25, 955-964.
38. McKeown, M. (1992). Alternative mRNA splicing. Annu. Rev. Cell Biol. 8, 133-155.
39. Milanesi, L., Kolchanov, N. A., Rogozin, I. B., Ischenko, I. V., Kel, A. E., Orlov, Yu. L., Ponomarenko, M. P., and Vezzoni, P. (1993). GenView: A computing tool for protein-coding regions prediction in nucleotide sequences. In Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis, H. A. Lim, J. W. Fickett, C. R. Cantor, and R. J. Robbins, Eds. (Singapore: World Scientific Publishing), pp. 573-588.
40. Nilsen, T. W. (1996). A parallel spliceosome Science 273, 1813.
41. Pavesi, A., Conterio, F., Boichi, A., Dieci, G., and Ottonello, S. (1994). Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions. Nucl. Acids Res. 22, 1247-1256.
42. Pedersen, A. G., Baldi, P., Brunak, S. and Chauvin, Y. (1996). Characterization of prokaryotic and eukaryotic promoters using hidden Markov models. In Fourth International Conference on Intelligent Systems in Molecular Biology, D. J. States, P. Agarwal, T. Gaasterland, L. Hunter, and R. Smith, eds. (Menlo Park, CA: AAAI Press), pp. 182-191.
43. Robison, K., Gilbert, W. and Church, G. M. (1994). Large scale bacterial gene discovery by similarity search. Nature Genet. 7, 205-214.
44. Rosenblueth, D. A., Thieffry, D., Huerta, A. M., Salgado, H., and Collado-Vides, J. (1996). Syntactic recognition of regulatory regions in Escherichia coli. Comput. Appl. Biosci. 12, 415-422.
45. Senapathy, P., Shapiro, M. B., and Harris, N. L. (1990). Splice junctions, branch point sites, and exons: Sequence statistics, identification, and applications to genome project. Methods Enzymol. 183, 252-278.
46. Smit, A. F. A. (1996). Origin of interspersed repeats in the human genome. Curr. Opin. Genet. Devl. 6, 743-749.
47. Smith, R. F., Wiese, B. A., Wojzynski, M. K., Davison, D. B., and Worley, K. C. (1996). BCM search launcher - An integrated interface to molecular biology data base search and analysis services available on the World Wide Web. Genome Res. 6, 454-462.
48. Snyder, E. E., and Stormo, G. D. (1995). Identification of coding regions in genomic DNA. J. Mol. Biol. 248, 1-18.
49. Snyder, E. E., and Stormo, G. D. (1996). Identifying genes in genomic DNA sequences. In DNA and Protein Sequence Analysis: A Practical Approach, M. J. Bishop and C. J. Rawlings, Eds. (Oxford: IRL Press), pp. 209-224.
50. Solovyev, V., and Salamov, A. (1997). The Gene-Finder computer tools for analysis of human and model organism genome sequences. In Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, T. Gaasterland, P. Karp, K. Karplus, C. Ousounis, C. Sander, and A. Valencia, Eds. (Menlo Park, CA: AAAI Press), pp. 294-302.
51. Stormo, G. D. (1990). Finding protein coding regions in genomic sequences. Methods Enzymol. 183, 211-220.
52. Tronche, F., Ringeisen, F., Blumenfeld, M., Yaniv, M., and Pontoglio, M. (1997). Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J. Mol. Biol. 266, 231-245.
53. von Hippel, P. H. (1994). Protein-DNA recognition: New perspectives and underlying themes. Science 263, 769-770.
54. Wahle, E., and Keller, W. (1996). The biochemistry of polyadenylation. Trends Biochem. Sci. 21, 247-250.
55. Xu, Y., Einstein, J. R., Mural, R. J., Shah, M., and Uberbacher, E. C. (1994). An improved system for exon recognition and gene modeling in human DNA sequences. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, R. Altman, D. Brutlag, P. Karp, R. Lathrop, and D. Searls, Eds. (Menlo Park, CA: AAAI Press), pp. 376-383.
56. Zhang, M. Q. (1997). Identification of protein coding regions in the human genome based on quadratic discriminant analysis. Proc. Natl. Acad. Sci. U.S.A. 94, 565-568.