Begin at the beginning: Predicting genes with 5′ UTRs

Genome Research

Volumn 15, Issue 5, 2005, Pages 742-747

  Brown, Randall H ^a   Gross, Samuel S ^a,b   Brent, Michael R ^a  

^a WASHINGTON UNIVERSITY   (United States)

^b Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

5' UNTRANSLATED REGION; ACCURACY; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; EXON; GENE STRUCTURE; GENETIC TRANSCRIPTION; GENETICS; GENOMICS; HUMAN; HUMAN GENETICS; INTRON; MATHEMATICAL COMPUTING; PREDICTION; PRIORITY JOURNAL; TRANSCRIPTION INITIATION SITE; VALIDATION PROCESS; BIOLOGICAL MODEL; BIOLOGY; DNA SEQUENCE; EVALUATION; GENE; GENOME; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; EVALUATION STUDIES; EXONS; GENES; GENOME, HUMAN; GENOMICS; HUMANS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION INITIATION SITE;

EID: 19844374535     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3696205     Document Type: Article

References (35)

1. Aerts, S., Thijs, G., Dabrowski, M., Moreau, Y., and De Moor, B. 2004. Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics 5: 34.
2. Bajic, B. and Seah, S. 2003. Dragon Gene Start Finder identifies approximate locations of the 5′ ends of genes. Nucleic Acids Res. 31: 3560-3563.
3. Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F., Roskin, R.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., et al. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14: 708-715.
4. Brent, M.R. 2002. Predicting full-length transcripts. Trends Biotechnol. 20: 273-275.
5. Brent, M.R. and Guigó, R. 2004. Recent advances in gene structure prediction. Curr. Opin. Struct. Biol. 14: 264-272.
6. 2-terminal kinase pathway. Science 280: 1945-1949.
7. Davuluri, R., Grosse, I., and Zhang, M. 2001. Computational identification of promoters and first exons in the human genome. Nat. Genet. 29: 412-417.
8. Down, T. and Hubbard, T. 2002. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12: 458-461.
9. Gross, S. and Brent, M. 2005. Using multiple alignments to improve gene prediction. The Ninth International Conference on Research in Computational Molecular Biology (RECOMB). (in press).
10. Hajarnavis, A., Kork, I., and Durbin, R. 2004. A probabilistic model of 3′ end formation in Caenorhabditis elegans. Nucl. Acids Res. 32: 3392-3399.
11. Hendrich, B. and Tweedie, S. 2003. The methyl-CpG binding domain and the evolving role of DNA methylation in animals. Trends Genet. 19: 269-277.
12. Holmes, I. and Bruno, W.J. 2001. Evolutionary HMMs: A Bayesian approach to multiple alignment. Bioinformatics 17: 803-820.
13. Isohikhes, I. and Zhang, M. 2000. Large-scale human promoter mapping using CpG islands. Nat. Genet. 26: 61-63.
14. Korf, I., Flicek, P., Duan, D., and Brent, M. 2001. Integrating genomic homology into gene structure prediction. Bioinformatics 17(Suppl 1): S140-S148.
15. Lee, J., Park, E.H., Couture, G., Harvey, I., Garneau, P., and Pelletier, J. 2002. An upstream open reading frame impedes translation of the huntingtin gene. Nucleic Acids Res. 30: 5110-5119.
16. Maruyama, K. and Sugano, S. 1994. Oligo-capping: A simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 200: 149-156.
17. McAuliffe, J.D., Pachter, L., and Jordan, M.I. 2004. Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics 20: 1850-1860.
18. Meyer, I. and Durbin, R. 2002. Comparative ab initio prediction of gene structures using pair HMMs. Bioinformatics 18: 1309-1318.
19. Miskimins, W., Wang, G., Hawkinson, M., and Miskimins, R. 2001. Control of cyclin-dependent kinase inhibitor p27 expression by cap-independent translation. Mol. Cell. Biol. 21: 4960-4967.
20. Rozen, S. and Skaletsky, H. 2000. Primer3 on the WWW for general users and biologist programmers. Methods Mol. Biol. 132: 365-386.
21. Scherf, M., Klingenhoff, A., and Werner, T. 2000. Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: A novel context analysis approach. J. Mol. Biol. 297: 599-606.
22. Siepel, A.C. and Haussler, D. 2004a. Computational identification of evolutionarily conserved exons. In RECOMB. ACM, San Diego, CA.
23. _. 2004b. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21: 468-488.
24. Suzuki, Y., Yamashita, R., Nakai, K., and Sugano, S. 2002. DBTSS: Data base of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 30: 328-331.
25. Yandell, M., Bailey, A.M., Misra, S., Shu, S., Wiel, C., Evans-Holm, M., Celniker, S.E., and Rubin, G.M. 2005. A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome. Proc. Natl. Acad. Sci. 102: 1566-1571.
26. http://genome.ucsc.edu; the July 2003 release of Build 34 (hg16) of the human genome, the human mRNA data base, and the FirstEF track of first exon predictions.
27. http://www.sanger.ac.uk/Users/td2/eponine; Eponine TSS finder.
28. http://sdmc.lit.org.sg/promoter/dragonGSF1_0/genestart.htm; DGSF.
29. http://www.rfcgr.mrc.ac.uk/Registered/Help/est_genome/; EST_GENOME.
30. http://dbtss.hgc.jp/index.html; Database of Human Transcription Start Sites home.
31. http://www.bdbiosciences.com; BD Biosciences home page.
32. http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi; Primer3.
33. http://www.ncbi.nimh.nih.gov/Traces
34. http://www.edgebio.com; Edge BioSystems home page.
35. http://genes.cse.wustl.edu/brown-05-UTR-data/; Supplemental data for this paper