Prediction of splice sites with dependency graphs and their expanded bayesian networks

Bioinformatics

Volumn 21, Issue 4, 2005, Pages 471-482

  Chen, Te Ming ^a   Lu, Chung Chin ^a   Li, Wen Hsiung ^b  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ACCURACY; ANALYTICAL ERROR; ARTICLE; BAYES THEOREM; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; EXON; GENE STRUCTURE; GENOME ANALYSIS; HUMAN; INTERNET; INTRON; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROMOTER REGION; PROTEIN PROCESSING; SEQUENCE ANALYSIS; SIGNAL DETECTION; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS; VALIDATION PROCESS;

BAYES THEOREM; GENE EXPRESSION PROFILING; MODELS, GENETIC; MODELS, STATISTICAL; RNA SPLICING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 14644392135     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti025     Document Type: Article

References (22)

1. Arita,M., Tsuda,K. and Asai,K. (2002) Modeling splicing sites with pairwise correlations. Bioinformatics, 18 (Suppl. 2), S27-S34.
2. Brunak,S., Engelbrecht,J. and Knudsen,S. (1991) Prediction of human mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol., 220, 49-65.
3. Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
4. Cai,D., Delcher,A., Kao,B. and Kasif,S. (2000) Modeling splice sites with Bayes networks. Bioinformatics, 16, 152-158.
5. Durbin,R., Eddy,S.R., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis: Probabilistic Models of Protein and Nucleic Acids. Cambridge University Press, Cambridge, MA.
6. Ewens,W.J. and Grant,G.R. (2001) Statistical Methods in Bioinformatics: An Introduction. Springer-Verlag, NY.
7. Hebsgaard,S.M., Korning,P.G., Tolstrup,N., Engelbrecht,J., Rouzé,P. and Brunak,S. (1996) Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res., 24, 3439-3452.
8. Henderson,J., Salzberg,S. and Fasman,K. (1997) Finding genes in human DNA with a hidden Markov model. J. Comput. Biol., 4, 127-141.
9. Khodarev,N.N., Park,J., Kataoka,Y., Nodzenski,E., Khorasani,L., Hellman,S., Roizman,B., Weichselbaum,R.R. and Pelizzari,C.A. (2003) Receiver operating characteristic analysis: a general tool for DNA array data filtration and performance estimation. Genomics, 81, 202-209.
10. Lander,E.S., Linton,L.M., Birren,B., Nusbaum,C., Zody,M.C. and Baldwin,J. Devon, K., Dewar, K., Doyle, M., and FitzHugh, W. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
11. Mathe,C., Sagot,M., Schiex,T. and Rouzé,P. (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res., 30, 4103-4117.
12. Mathews,C.K., van Holde,K.E. and Ahem,K.G. (2000) Biochemistry, 3rd edn. Addison Wesley Longman, San Francisco, CA.
13. Pearl,J. (1988) Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference. Morgan Kaufmann, San Mateo, CA.
14. Pertea,M., Lin,X. and Salzberg,S.L. (2001) GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res. 29, 1185-1190.
15. Reese,M.G., Eeckman,F.H., Kulp,D. and Haussler,D. (1997) Improved splice site recognition in Genie. J. Comput. Biol., 4 311-324.
16. Salzberg,S., Delcher,A., Fasman,K. and Henderson,J. (1998) A decision tree system for finding genes in DNA. J. Comput. Biol., 5, 667-680.
17. Staden,R. (1984) Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res., 12, 505-519.
18. Tolstrup,N., Rouzé,P. and Brunak,S. (1997) A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res., 25 3159-3163.
19. Weaver,R.F. (1999) Molecular Biology. WCB McGraw-Hill, NY.
20. Yeo,G. and Burge,C.B. (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol., 11, 377-394.
21. Zhang,M.Q. (2002) Computational prediction of eukaryotic protein-coding genes. Nat. Rev. Genet., 3, 698-709.
22. Zhang,M.Q. and Marr,T.G. (1993) A weight array method for splicing signal analysis. Comput. Appl. Biosci., 9, 499-509.