Integrating genomic homology into gene structure prediction

Bioinformatics

Volumn 17, Issue SUPPL. 1, 2001, Pages

  Korf, Ian ^a   Flicek, Paul ^a   Duan, Daniel ^a   Brent, Michael R ^a  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGY; COMPARATIVE STUDY; EVALUATION; GENETICS; GENOME; HUMAN; MOLECULAR EVOLUTION; MOUSE; NUCLEOTIDE SEQUENCE; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STATISTICAL MODEL; STATISTICS;

ALGORITHMS; ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DNA; EVOLUTION, MOLECULAR; GENOME; GENOME, HUMAN; HUMANS; MICE; MODELS, STATISTICAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 17444437765     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.suppl_1.S140     Document Type: Article

References (26)

1. Ansari-Lari, M. A., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1998). Comparative sequence anlaysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome Research, 8, 29-40.
2. Bafna, V. & Huson, D. H. (2000). The conserved exon method for gene finding. In Proceedings from the Eigth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, pp. 3-12.
3. Batzoglou, S., Pachter, L., Mesirov, J. P., Berger, B. & Lander, E. S. (2000). Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Research, 10, 950-958.
4. Burge, C. (1997). Identification of genes in human genomic DNA. Ph.D. thesis, Stanford University.
5. Burge, C. & Karlin, S. (1997). Prediction of complete gene structures in genomic DNA. Journal of Molecular Biology, 268, 78-94.
6. Burset, M. & Guigo, R. (1996). Evaluation of gene structure prediction programs. Genomics, 34, 353-367.
7. Gaasterland, T., Sczyrba, A., Thomas, E., Aytekin-Kurban, G., Gordon, P. & Sensen, C. W. (2000). MAGPIE/EGRET annotation of the 2.9-mb Drosophila melanogaster Adh region. Genome Research, 10, 502-510.
8. Gelfand, S., Mironov, A. A. & Pevzner, P. A. (1996). Gene recognition via spliced sequence alignment. PNAS USA, 93, 9061-9066.
9. Hardison, R. C., Oeltjen, J. & Miller, W. (1997). Long human-mouse sequence alignments reveal novel regulatory elments: a reason to sequence the mouse genome. Genome Research, 7, 959-966.
10. Hooper, P. M., Zhang, H. & Wishart, D. S. (2000). Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment. Bioinformatics, 16, 425-438.
11. Jang, W., Hua, A., Spilson, S. V., Miller, W., Roe, B. A. & Meisler, M. H. (1999). Comparative sequence of human and mouse BAC clones from the mnd region of chromosome 2p13. Genome Research, 9, 53-61.
12. Jareborg, N., Birney, E. & Durbin, R. (1999). Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Research, 9, 815-824.
13. Kent, W. J. & Zahler, A. M. (2000). Conservation, regulation, synteny, and introns in a large-scale C. elegans-C. briggsae genomic alignment. Genome Research, 10, 1115-1125.
14. Krogh, A. (1997). Two methods for improving performance of an HMM and their application for gene finding. In Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, pp. 179-186.
15. Krogh, A. (2000). Using database matches with HMMGene for automated gene detection in Drosophila. Genome Research, 10, 523-528.
16. Kulp, D., Haussler, D., Reese, M. G. & 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. AAAI Press, pp. 134-142.
17. Meyer, A. & Schartl, M. (1999). Gene and genome duplications in vetebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Current Opinions in Cell Biology, 11, 699-704.
18. Oeltjen, J. C., Malley, T. M., Muzny, D. M., Miller, W., Gibbs, R. A. & Belmont, J. W. (1997). Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Research, 7, 315-329.
19. Parra, G., Blanco, E. & Guigo, R. (2000). GeneID in Drosphila. Genome Research, 10, 511-515.
20. Reese, M., Hartzell, G., Harris, N., Ohler, U., Abril, J. & Lewis, S. (2000a). Genome annotation assessment in Drosphila melanogaster. Genome Research, 10, 483-501.
21. Reese, M., Kulp, D., Tammana, H. & Haussler, D. (2000b). Genie-gene finding in Drosophila melanogaster. Genome Research, 10, 529-538.
22. Salamov, A. A. & Solovyev, V. V. (2000). Ab initio gene finding in Drosophila genomic DNA. Genome Research, 10, 516-522.
23. Salzberg, S. (1997). A method for identifying splice sites and translational start sites in eukaryotic mRNA. Computer Applications in the Biosciences, 13, 365-376.
24. Xu, Y., Mural, R. J. & Uberbacher, E. C. (1997). Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags. In Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, pp. 344-353.
25. Yeh, R. F., Lim, L. P. & Burge, C. B. (2001). Computational inference of homologous gene structures in the human genome. Genome Research, 11, 803-816.
26. Zhang, M. & Marr, T. (1993). A weight array method for splicing signal analysis. Computer Applications in the Biosciences, 9, 499-509.