Using multiple alignments to improve gene prediction

Journal of Computational Biology

Volumn 13, Issue 2, 2006, Pages 379-393

  Gross, Samuel S ^a,b   Brent, Michael R ^a  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Comparative genomics; Gene prediction; Genome annotation; Phylogenetic models

Indexed keywords

DNA;

ACCURACY; BAYES THEOREM; CALCULATION; COMPUTER PROGRAM; CONFERENCE PAPER; DROSOPHILA MELANOGASTER; GENE DELETION; GENE INSERTION; GENE PREDICTION; GENE SEQUENCE; GENOME ANALYSIS; HUMAN; HUMAN GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROBABILITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SPECIES; STRUCTURE ANALYSIS;

ANIMALS; DATABASES, FACTUAL; DNA; DROSOPHILA MELANOGASTER; EXONS; GENOME; HUMANS; MODELS, GENETIC; PREDICTIVE VALUE OF TESTS; SEQUENCE ALIGNMENT; SOFTWARE;

DROSOPHILA MELANOGASTER;

EID: 33645979674     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2006.13.379     Document Type: Conference Paper

References (22)

1. Alexandersson, M., Cawley, S., and Pachter, L. 2003. SLAM: Cross-species gene finding and alignment with a generalized pair hiddden Markov model. Genome Res. 13, 496-502.
2. Blanchett, M., et al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715.
3. Brown, R.H., Gross, S.S., and Brent, M.R. 2005. Begin at the beginning: Predicting genes with 5′ UTRs. Genome Res. 15, 742-747.
4. Bulmer, M. 1986. Neighboring base effects on substitution rates in pseudogenes. Mol. Biol. Evol. 3, 322-329.
5. Burge, C., and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94.
6. Felsenstein, J. 1982. Evolutionary trees from DNA sequences. J. Mol. Evol. 17, 368-376.
7. Flicek, P., Keibler, E., Hu, P., Korf, I., and Brent, M.R. 2003. Leveraging the mouse genome for gene prediction in human. Genome Res. 13, 46-54.
8. Gerhard, D., et al. 2004. The status, quality, and expansion of the NIH full-length cDNA project: The mammalian gene collection (MGC). Genome Res. 14, 2121-2127.
9. Kent, W., Sugnet, C., Furey, T., Roskin, K., Pringle, T., Zahler, A., and Haussler, D. 2003. The human genome browser at UCSC. Genome Res. 12, 996-1006.
10. Korf, I., Flicek, P., Duan, D., and Brent, M.R. 2001. Integrating genomic homology into gene structure prediction. Bioinformatics 17(Suppl. 1), S140-148.
11. Lió, P., and Goldman, N. 1998. Models of molecular evolution and phylogeny. Genome Res. 8, 1233-1244.
12. McAuliffe, J., Pachter, L., and Jordan, M.I. 2003. Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Technical report 647, Department of Statistics, University of California, Berkeley.
13. Parra, G., Agarwal, P., Abril, J., Wiehe, T., Fickett, J., and Guigo, R. 2003. Comparative gene prediction in human and mouse. Genome Res. 13, 108-117.
14. Pedersen, J., and Hein, J. 2003. Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics 19, 219-227.
15. Siepel, A.C., and Haussler, D. 2004a. Computational identification of evolutionarily conserved exons. Proc. 8th Ann. Conf. on Research in Computational Molecular Biology (RECOMB '04).
16. Siepel, A.C., and Haussler, D. 2004b. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21, 448-468.
17. Stanke, M., and Waack, S. 2003. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19(Suppl. 2), ii215-ii225.
18. Tenney, A.E., Brown, R.H., Vaske, C., Lodge, J., Doering, T.L., and Brent, M.R. 2004. Gene prediction and verification in a compact genome with many small introns. Genome Res. 14, 2330-2335.
19. Wang, J., et al. 2003a. Vertebrate gene prediction and the problem of large genes. Nature Rev. Genet. 4(9), 741-749.
20. Wang, M., Buhler, J., and Brent, M.R. 2003b. The effects of evolutionary distance on TWINSCAN, an algorithm for pair-wise comparative gene prediction. Cold Spring Harbor Symp. Quant. Biol 68, 125-130.
21. Waterston, R.H., et al. 2002. Initial sequencing and comparitive analysis of the mouse genome. Nature 420, 520-562.
22. Zhang, L., Pavlovic, V., Cantor, C., and Kasif, S. 2003. Human-mouse gene identification by comparative evidence integration and evolutionary analysis. Genome Res. 13, 1190-1202.