GlimmerM, Exonomy and Unveil: Three ab initio eukaryotic genefinders

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3601-3604

  Majoros, William H ^a   Pertea, Mihaela ^a   Antonescu, Corina ^a   Salzberg, Steven L ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; ARABIDOPSIS; ARTICLE; COMPUTER PROGRAM; DECISION THEORY; GENE IDENTIFICATION; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; INTERNET; NONHUMAN; PERFORMANCE; PREDICTION; PRIORITY JOURNAL; PROBABILITY; STANDARD; DNA SEQUENCE; EUKARYOTIC CELL; EXON; GENE; GENETICS; INTRON; METHODOLOGY;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EUKARYOTA;

ARABIDOPSIS; EUKARYOTIC CELLS; EXONS; GENES; GENES, PLANT; INTERNET; INTRONS; MARKOV CHAINS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 0041620262     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg527     Document Type: Article

References (16)

1. Das,M., Burge,C.B., Park,E., Colinas,J. and Pellitier,J. (2001) Assessment of the total number of human transcription units. Genomics, 77, 71-78.
2. Guigo,R., Dermitzakis,E.T., Agarwal,P., Ponting,C.P., Parra,G., Reymond,A., Abril,J.F., Keibler,E., Lyle,R., Ucla,C., Antonarakis,S.T. and Brent,M.R. (2003) Comparison of mouse and human genomes followed by experimental verification yields an estimated 1019 additional genes. Proc. Natl Acad. Sci. USA, 100, 1140-1145.
3. Salzberg,S.L., Delcher,A.L., Kasif,S. and White,O. (1998) Microbial gene identification using interpolated Markov models. Nucleic Acids Res., 26, 544-548.
4. Salzberg,S.L., Searls,D.B. and Kasif,S. (eds). (1998) Computational Methods in Molecular Biology. Elsevier, Amsterdam, The Netherlands.
5. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge, UK.
6. MatheÌC., Sagot,M.-F., Schiex,T. and RouzeÌP. (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res., 30, 4103-4117.
7. Salzberg,S.L., Pertea,M., Delcher,A.L., Gardner,M.J. and Tettelin,H. (1999) Interpolated Markov models for eukaryotic gene finding. Genomics, 59, 24-31.
8. Pertea,M., Lin,X. and Salzberg,S.L. (2001) GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res., 29, 1185-1190.
9. Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
10. Murthy,S.K., Kasif,S. and Salzberg,S.L. (1994) A system for induction of oblique decision trees. J. Artificial Intelligence Res., 2, 1-32.
11. Henderson,J., Salzberg,S. and Fasman,K.H. (1997) Finding genes in DNA with a Hidden Markov Model. J. Comput. Biol., 4, 127-141.
12. Baum,L.E., Petrie,T., Soules,G. and Weiss,N. (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann. Math. Stat., 41, 164-171.
13. Viterbi,A.J. (1967) Error bounds for convolutional codes and an asymptotically optimal decoding algorithm. IEEE Trans. Information Theory, 13, 260-269.
14. Reese,M.G., Kulp,D., Tammana,H. and Haussler,D. (2000) Genie - gene finding in Drosophila melanogaster. Genome Res., 4, 529-538.
15. Haas,B.J., Volfovsky,N., Town,C.D., Troukhan,M., Alexandrov,N., Feldmann,K.A., Flavell,R.B., White,O. and Salzberg,S.L. (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol., 3, 1-12.
16. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.