ExonHunter: A comprehensive approach to gene finding

Bioinformatics

Volumn 21, Issue SUPPL. 1, 2005, Pages

  Brejová, Broňa ^a   Brown, Daniel G ^a   Li, Ming ^a   Vinař, Tomáš ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENOME ANALYSIS; HUMAN; INFORMATION PROCESSING; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN DATABASE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EXISTING SYSTEMS; EXPRESSED SEQUENCE TAGS; GENE FINDING; GENOMIC SEQUENCE; INTERGENIC REGIONS; LENGTH DISTRIBUTIONS; MISSING INFORMATION; PROTEIN DATABASE; QUADRATIC PROGRAMMING METHOD; ROSETTA; TEST SETS;

HIDDEN MARKOV MODELS; INTELLIGENT SYSTEMS; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE;

GENES;

EID: 29144445262     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1040     Document Type: Article

References (31)

1. Alexanderson,M., Cawley,S. and Pachter,L. (2003) SLAM: Crossspecies gene finding and alignment with a generalized pair hidden Markov model. Genome Res., 13, 496-502.
2. Allen,J.E., Pertea,M. and Salzberg,S.L. (2004) Computational gene prediction using multiple sources of evidence. Genome Res., 14, 142-148.
3. Batzoglou,S., Pachter,L., Mesirov,J.P., Berger,B. and Lander,E.S. (2000) Human and mouse gene structure: Comparative analysis and application to exon prediction. Genome Res., 10, 950-958.
4. Brejova,B., Brown,D.G. and Vinar,T. (2003) Optimal DNA signal recognition models with a fixed amount of intrasignal dependency. In Algorithms and Bioinformatics: 3rd International Workshop (WABI), vol. 2812 of LNBI, pp. 78-94.
5. Brejova,B., Brown,D.G. and Vinar,T. (2004) Optimal spaced seeds for homologous coding regions. J. Bioinform. Comput. Biol., 1, 595-610.
6. Brejova,B. and Vinar,T. (2002) A better method for length distribution modeling in HMMs and its application to gene finding. In Combinatorial Pattern Matching (CPM), vol. 2373 of LNCS, pp. 190-202.
7. Brent,M.R. and Guigo,R. (2004) Recent advances in gene structure prediction. Curr. Opin. Struct. Biol., 14, 264-272.
8. Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
9. Chatterji,S. and Pachter,L. (2004) Multiple organism gene finding by collapsed Gibbs sampling. In International Conference on Computational Molecular Biology (RECOMB), pp. 187-193.
10. Fletcher,R. (1987) Practical Methods of Optimization. Wiley, Chichester, UK.
11. Florea,L., Hartzell,G., Zhang,Z., Rubin,G.M. and Miller,W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8, 967-974.
12. Fulton,T., Kasif,S. and Salzberg,S. (1995) Efficient algorithms for finding multi-way splits for decision trees. In International Conference on Machine Learning (ICML), pp. 244-251.
13. Gish,W. and States,D.J. (1993) Identification of protein coding regions by database similarity search. Nat. Genet., 3, 266-272.
14. Iseli,C., Jongeneel,C.V. and Bucher,P. (1999) ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In International Conference on Intelligent Systems for Molecular Biology (ISMB), pp. 138-148.
15. Keibler,E. and Brent,M.R. (2003) Eval: A software package for analysis of genome annotations. BMC Bioinformatics, 4, 50.
16. Korf,I., Flicek,P., Duan,D. and Brent,M.R. (2001) Integrating genomic homology into gene structure prediction. Bioinformatics, 17 (Suppl. 1), S140-S148.
17. Krogh,A. (2000) Using database matches with for HMMGene for automated gene detection in Drosophila. Genome Res., 10, 523-528.
18. Kulp,D., Haussler,D., Reese,M.G. and Eeckman,F.H. (1997) Integrating database homology in a probabilistic gene structure model. In Pacific Symposium on Biocomputing (PSB), pp. 232-234.
19. Ma,B., Tromp,J. and Li,M. (2002) PatternHunter: Faster and more sensitive homology search. Bioinformatics, 18, 440-445.
20. Meyer,I.M. and Durbin,R. (2004) Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res., 32, 776-783.
21. 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.
22. Rat Genome Sequencing Project Consortium. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428, 493-521.
23. Schiex,T., Moisan,A. and Rouzé,P. (2000) EUGÈNE: An eukaryotic gene finder that combines several sources of evidence. In Computational Biology. Selected papers from First International Conference on Biology, Informatics, and Mathematics, vol. 2066 of LNCS, pp. 111-125.
24. Shafer,G.A. (1976) Mathematical theory of evidence. Princeton University Press, Princeton, NJ.
25. Siepel,A. and Haussler,D. (2004) Computational identification of evolutionarily conserved exons. In International Conference on Computational Molecular Biology (RECOMB), pp. 177-186.
26. Smit,A.F.A., Hubley,R. and Green,P. (2002). RepeatMasker, www.repeatmasker.org.
27. Stanke,M. and Waack,S. (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics, 19 (Suppl. 2), II215-II225.
28. Tax,D.M.J., van Breukelen,M., Duin,R.P.W. and Kittler,J. (2000) Combining multiple classifiers by averaging or multiplying? Pattern Recogn., 33, 1475-1485.
29. Thomas,J.W. et al. (2003) Comparative analyses of multispecies sequences from targeted genomic regions. Nature, 424, 788-793.
30. Xu,Y. and Uberbacher,E.C. (1997) Automated gene identification in large-scale genomic sequences. J. Comput. Biol., 4, 325-328.
31. Yeh,R.F., Lim,L.P. and Burge,C.B. (2001) Computational inference of homologous gene structures in the human genome. Genome Res., 11, 803-806.