GAZE: A genetic framework for the integration of gene-prediction data by dynamic programming

Genome Research

Volumn 12, Issue 9, 2002, Pages 1418-1427

  Howe, Kevin L ^a   Chothia, Tom ^a   Durbin, Richard ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; COMPUTER PROGRAM; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE SEQUENCE; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC MODEL; GENOME SIZE; PREDICTION; PRIORITY JOURNAL; PROBABILITY; RNA SPLICING; SCORING SYSTEM; SEQUENCE ALIGNMENT; TRANS ISOMER; VALIDATION PROCESS; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; FACTUAL DATABASE; FORECASTING; GENE; GENETICS; GENOME; INFORMATION RETRIEVAL; INTERNET; METHODOLOGY; SEQUENCE HOMOLOGY; SEQUENCE TAGGED SITE; STATISTICS; TRANS SPLICING;

CAENORHABDITIS; CAENORHABDITIS ELEGANS;

HELMINTH RNA;

ALGORITHMS; ANIMALS; CAENORHABDITIS ELEGANS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; FORECASTING; GENES, HELMINTH; GENOME; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MODELS, GENETIC; PROBABILITY; RNA, HELMINTH; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; SEQUENCE TAGGED SITES; SOFTWARE; TRANS-SPLICING;

EID: 0036708637     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.149502     Document Type: Article

References (21)

1. Blumenthal, T. and Steward, K. 1997. RNA processing and gene structure. In C. elegans II (eds. D.L. Riddle et. al), pp. 117-145. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
2. Burge, C. and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-94.
3. Burge, C. and Karlin, S. 1998. Finding the genes in genomic DNA. Curr. Opin. Struct. Biol. 8: 346-354.
4. Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. 1998. Biological sequence analysis: Probabilistic models of proteins and nucleic acids (Chapter 3). Cambridge University Press, Cambridge, UK.
5. Guigó, R. 1998. Assembling genes from predicted exons in linear time with dynamic programming. J. Comp. Biol. 5: 681-702.
6. Guigó, R., Knudsen, S.N.D., and Smith, T. 1992. Prediction of gene structure. J. Mol. Biol. 226: 141-157.
7. Guigó, R., Agarwal, P., Abril, J.F., Burset, M., and Fickett, J.W. 2000. An assessment of gene prediction accuracy in large DNA sequences. Genome Res. 10: 1631-1642.
8. Krause, M. and Hirsh, D. 1987. A trans-spliced leader sequence on actin mRNA in C. elegans. Cell 49: 753-761.
9. Krogh, A. 1997. Two methods for improving performance of a HMM and their application for gene finding. Proc. Intell. Syst. Mol. Biol. 5: 179-186.
10. Krogh, A. 2000. Using database matches with HMMGene for automated gene detection on Drosophila. Genome Res. 10: 523-528.
11. Kulp, D., Haussler, D., Reese, M.G., and Eeckman, F.H. 1996. A generalized hidden Markov model for the recognition of human genes in DNA. Proc. Intell. Syst. Mol. Biol. 4: 134-142.
12. Mott, R. 1997. EST GENOME: A program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci. 13: 477-478.
13. Rabiner, L.R. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77: 257-286.
14. Reese, M.G., Hartzell, G., Harris, N.L., Ohler, U., Abril, J.F., and Lewis, S.E. 2000a. Genome annotation assessment in Drosophila. Genome Res. 10: 483-501.
15. Reese, M.G., Kulp, D., Tammana, H., and Haussler, D. 2000b. Genie: Gene-finding in Drosophila melanogaster. Genome Res. 10: 529-538.
16. Salamov, A.A. and Solovyev, V.V. 2000. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10: 516-522.
17. Solovyev, V.V., Salamov, A.A., and Lawrence, C.B. 1995. Identification of human gene structure using linear discriminant functions and dynamic programming. Proc. Intell. Syst. Mol. Biol. 3: 367-375.
18. Stormo, G.D. 2000. Gene-finding approaches for eukaryotes. Genome Res. 10: 394-397.
19. Stormo, G.D. and Haussler, D. 1994. Optimally parsing a sequence into different classes based on multiple types of evidence. Proc. Intell. Syst. Mol. Biol. 4: 369-375.
20. Xu, Y., Mural, R.J., and Uberbacher, E.C. 1994. Constructing gene models from accurately predicted exons: An application of dynamic programming. Comput. Appl. Biosci. 10: 613-623.
21. Yeh, R.F., Burge, Lim, L.P., Burge, C.B. 2001. Computational inference of homologous gene structures in the human genome. Genome Res. 11: 803-816.