Dragon gene start finder: An advanced system for finding approximate locations of the start of gene transcriptional units

Genome Research

Volumn 13, Issue 8, 2003, Pages 1923-1929

  Bajic, Vladimir B ^a   Seah, Seng Hong ^a  

^a INSTITUTE FOR INFOCOMM RESEARCH   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE; NUCLEOTIDE;

ACCURACY; ARTICLE; CHROMOSOME 21; CHROMOSOME 22; CHROMOSOME 4; CHROMOSOME ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; CPG ISLAND; GENE LOCATION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; HUMAN; MAMMAL; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION SITE;

MAMMALIA;

EID: 0042525750     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.869803     Document Type: Article

References (32)

1. Bajic, V.B. 2000. Comparing the success of different prediction software in sequence analysis: A review. Brief. Bioinform. 1: 214-228.
2. Bajic, V.B., Seah, S.H., Chong, A., Zhang, G., Koh, J.L.Y., and Brusic, V. 2002a. Dragon Promoter Finder: Recognition of vertebrate RNA Polymerase II promoters. Bioinformatics 18: 198-199.
3. Bajic, V.B., Chong, A., Seah, S.H., and Brusic, V. 2002b. Intelligent System for Vertebrate Promoter Recognition. IEEE Intelligent Systems 17: 64-70.
4. Bajic, V.B., Seah, S.H., Chong, A., Krishnan, S.P.T., Koh, J.L.Y., and Brusic, V. 2003. Computer model for recognition of functional transcription start sites in polymerase II promoters of vertebrates. J. Mol. Graph. Model. 21: 323-332.
5. Bird, A.P., Taggart, M.H., Nichollas, R.D., and Higgs, D.R. 1986. Non-methylated CpG-rich islands at the human α-globin locus: Implications for evolution of the α-globin pseudogene. EMBO J. 6: 999-1004.
6. Bishop, C.M. 1995. Neural networks for pattern recognition. Clarendon Press, Oxford, UK.
7. Chong, A., Zhang, G., and Bajic, V.B. 2002. Information and sequence extraction around the 5′-end and translation initiation site of human genes. In Silico Biol. 2: 461-465.
8. Collins, J.E., Goward, M.E., Cole, C.G., Smink, L.J., Huckle, E.J., Knowles, S., Bye, J.M., Beare, D.M., and Dunham, I. 2003. Reevaluating human gene annotation: A second-generation analysis of chromosome 22. Genome Res. 13: 27-36.
9. Cross, S.H. and Bird, A.P. 1995. CpG islands and genes. Curr. Opin. Genet. Dev. 5: 309-314.
10. Cross, S.H., Clark, V.H., and Bird, A.P. 1999. Isolation of CpG islands from large genomic clones. Nucleic Acids Res. 27: 2099-2107.
11. Davuluri, R.V., Grosse, I., and Zhang, M.Q. 2001. Computational identification of promoters and first exons in the human genome. Nat. Genet. 29: 412-417.
12. Down, T.A. and Hubbard, T.J. 2002. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12: 458-461.
13. Fickett, J.W. and Hatzigeorgiou, A.G. 1997. Eukaryotic promoter recognition. Genome Res. 7: 861-878.
14. Gardiner-Garden, M. and Frommer, M. 1987. CpG islands in vertebrate genomes. J. Mol. Biol. 196: 261-282.
15. Hannenhalli, S. and Levy, S. 2001. Promoter prediction in the human genome. Bioinformatics 17: S90-S96.
16. Ioshikhes, I.P. and Zhang, M.Q. 2000. Large-scale human promoter mapping using CpG islands. Nat. Genet. 26: 61-63.
17. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
18. Larsen, F., Gundersen, G., Lopez, R., and Prydz, H. 1992. CpG islands as gene markers in the human genome. Genomics 13: 1095-1107.
19. Maruyama, K. and Sugano, S. 1994. Oligo-capping: A simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138: 171-174.
20. Pedersen, A.G., Baldi, P., Chauvin, Y., and Brunak, S. 1999. The biology of eukaryotic promoter prediction - A review. Comput. Chem. 23: 191-207.
21. Ponger, L. and Mouchiroud, D. 2002. CpGProD: Identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics 18: 631-633.
22. Ponger, L., Duret, L., and Mouchiroud, D. 2001. Determination of CpG islands: Expression in early embryo and isochore structure. Genome Res. 11: 1854-1860.
23. Prestridge, D.S. 2000. Computer software for eukaryotic promoter analysis. Review. Methods Mol. Biol. 130: 265-295.
24. Scherf, M., Klingenhoff, A., and Werner, T. 2000. Highly specific localisation of promoter regions in large genomic sequences by PromoterInspector: A novel context analysis approach. J. Mol. Biol. 297: 599-606.
25. Scherf, M., Klingenhoff, A., Frech, K., Quandt, K., Schneider, R., Grote, K., Frisch, M., Gailus-Durner, V., Seidel, A., Brack-Werner, R., et al. 2001. First pass annotation of promoters on human chromosome 22. Genome Res. 11: 333-340.
26. Sha, D. and Bajic, V.B. 2002. On-line hybrid learning algorithm for MLP in identification problems. Computers and Electrical Engineering 28: 587-598.
27. Stormo, G.D. 2000. Gene-finding approaches for eukaryotes. Genome Res. 10: 394-397.
28. Suzuki, Y., Yoshitomo-Nakagawa, K., Maruyama, K., Suyama, A., and Sugano, S. 1997. Construction and characterization of a full length-enriched and a 5′-end-enriched cDNA library. Gene 200: 149-156.
29. Suzuki, Y., Taira, H., Tsunoda, T., Mizushima-Sugano, J., Sese, J., Hata, H., Ota, T., Isogai, T., Tanaka, T., Morishita, S., et al. 2001. Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep. 2: 388-393.
30. Suzuki, Y., Yamashita, R., Nakai, K., and Sugano. S. 2002. DBTSS: DataBase of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 30: 328-331.
31. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
32. Werner, T. 2002. Finding and decrypting of promoters contributes to elucidation of gene functions. In Silico Biol. 2: 249-255.