GeneWise and Genomewise

Genome Research

Volumn 14, Issue 5, 2004, Pages 988-995

  Birney, Ewan ^a   Clamp, Michele ^a   Durbin, Richard ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; RNA;

ARTICLE; COMPUTER PREDICTION; COMPUTER SYSTEM; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DNA FLANKING REGION; EXPRESSED SEQUENCE TAG; GENE DELETION; GENE INSERTION SEQUENCE; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC MODEL; GENEWISE; GENOMEWISE; PRIORITY JOURNAL; PROTEIN DATABASE; RNA SPLICING; SEQUENCE ANALYSIS;

3' FLANKING REGION; 5' FLANKING REGION; ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA, COMPLEMENTARY; MODELS, THEORETICAL; PREDICTIVE VALUE OF TESTS; RESEARCH DESIGN; SOFTWARE;

EID: 2442713832     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1865504     Document Type: Article

References (28)

1. Alexandersson, M., Cawley, S., and Pachter, L. 2003. SLAM: Cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res. 13: 496-502.
2. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.-M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310.
3. Birney, E. and Durbin, R. 1997. Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison. ISMB 97: 56-64.
4. Birney, E. and Durbin, R. 2000. Using GeneWise in the Drosophila annotation experiment. Genome Res. 10: 547-548.
5. Birney, E., Thompson, J.D., and Gibson, T.J. 1996. Pairwise and searchwise: Comparison of a protein profile to all three translation frames simultaneously. Nucleic Acids Res. 24: 2730-2739.
6. Burge, C. and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-94.
7. Curwen, V., Eyras, E., Andrews, D., Clarke, L., Mongin, E., Searle, S., and Clamp, M. 2004. The ensembl automatic gene annotation system. Genome Res. (this issue).
8. Dehal, P., Satou, Y., Campbell, R.K., Chapman, J., Degnan, B., De Tomaso, A., Davidson, B., Di Gregorio, A., Gelpke, M., Goodstein, D.M., et al. 2002. The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298: 2157-2167.
9. Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763.
10. Flicek, P., Keibler, E., Hu, P., Korf, I., and Brent, M.R. 2003. Leveraging the mouse genome for gene prediction in human: From whole-genome shotgun reads to a global synteny map. Genome Res. 13: 46-54.
11. Galagan, J.E., Calvo, S.E., Borkovich, K.A., Selker, E.U., Read, N.D., Jaffe, D., FitzHugh, W., Ma, L.-J., Smirnov, S., Purcell, S., et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
12. Gelfand, M.S., Mironov, A.A., and Pevzner, P.A. 1996. Gene recognition via spliced sequence alignment. Proc. Natl. Acad. Sci. 93: 9061-9066.
13. Guigo, 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.
14. Hillier, L.W., Fulton, R.S., Fulton, L.A., Graves, T.A., Pepin, K.H., Wagner-McPherson, C., Layman, D., Maas, J., Jaeger, S., Walker, R., et al. 2003. The DNA sequence of human chromosome 7. Nature 424: 157-164.
15. Holmes, I. and Durbin, R. 1998. Dynamic programming alignment accuracy. J. Comp. Biol. 5: 493-504.
16. Howe, K.L., Chothia, T., and Durbin, R. 2002. GAZE: A generic framework for the integration of gene-prediction data by dynamic programming. Genome Res. 12: 1418-1427.
17. The International Human Genome Sequencing Consortium 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
18. Krogh, A. 2000. Using database matches with HMMGene for automated gene detection in Drosophila. Genome Res. 10: 523-528.
19. 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. In Proceedings of the fourth international conference on intelligent systems for molecular biology (eds. D.J. States et al.), pp. 134-142. AAAI Press, Menlo Park, CA.
20. Meyer, I.M. and Durbin, R. 2002. Comparative ab initio prediction of gene structures using pair HMMs. Bioinformatics 18: 1309-1318. Evaluation Studies.
21. Mott, R. 1997. EST-GENOME: A program to align spliced DNA sequences to unspliced genomic DNA. Comp. Appl. Biosci. 13: 477-478.
22. Parra, G., Agarwal, P., Abril, J.F., Wiehe, T., Fickett, J.W., and Guigo, R. 2003. Comparative gene prediction in human and mouse. Genome Res. 13: 108-117.
23. Pedersen, J.S. and Hein, J. 2003. Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics 19: 219-227.
24. Siepel, A. and Haussler, D. 2003. Combining phylogenetic and hidden markov models in biosequence analysis. In Proceedings of the seventh annual international conference on research in computational biology (RECOMB'03) 277-286.
25. Solovyev, V.V. and Salamov, A.A.S. 1997. The Gene-Finder computer tools for analysis of human and model organisms genome sequences. ISMB 97: 294-302.
26. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P. et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
27. Yeh, R.F., Lim, L.P., and Burge, C.B. 2001. Computational inference of homologous gene structures in the human genome. Genome Res. 11: 803-816.
28. Zhang, M.Q. 2002. Computational prediction of eukaryotic protein-coding genes. Nat. Rev. Genet. 3: 698-709.