Exon prediction in eucaryotic genomes

Biochimie

Volumn 78, Issue 5, 1996, Pages 327-334

  Vignal, L ^a   D'Aubenton Carafa, Y ^b   Lisacek, F ^b,c   Mephu Nguifo, E ^d   Rouze P ^e   Quinqueton, J ^a,f   Thermes, C ^b  

^a LIRMM   (France)

^b CNRS   (France)

^c LABORATOIRE DES SCIENCES DU CLIMAT ET DE L ENVIRONNEMENT   (France)

^d Centre de Recherche en Informatique de Lens   (France)

^e DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^f INRIA ROCQUENCOURT   (France)

Author keywords

Computer method; Exon; Gene coding region; Intron; Models; Prediction; Splice site

Indexed keywords

PLANT DNA;

ARTICLE; BINDING SITE; COMPUTER SYSTEM; EXON; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT; PREDICTION; RNA SPLICING;

EUKARYOTA;

EID: 0029845522     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/0300-9084(96)84765-1     Document Type: Article

References (23)

1. 1 Rymond BC, Rosbash M (1992) In: Yeast pre-mRNA splicing (Jones EW, Pringle JR, Broach JR, eds). Cold Spring Harbour Laboratory, New York
2. 2 Woolford JJ (1989) Nuclear pre-mRNA splicing in Yeast. Yeast 5, 439-457
3. 3 Sharp P (1993) Splicing of precursors to mRNA by the spliceosome. In: RNA World (Gesteland RF, Atkins JF, eds) Cold Spring Harbor Laboratory Press, 303-357
4. 4 Senapathy P, Shapiro MB, Harris NL, (1990) Splice junctions, branch point sites, and exons. Methods Enzymol 183, 252-280
5. 5 Filipowicz W, Gniadkowski M, Klahre U, Liu HX (1994) In: Pre-mRNA Processing (Lamond A, ed) RG Landes Publishers, Georgetown TX, 65-77
6. 6 Kalogeropoulos A (1995) Automatic intron detection in nuclear DNA sequences of Saccharomyces cerevisiae. Yeast 11, 555-565
7. 7 Solovyev VV, Salamov AA, Lawrence CB (1994) Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res 22, 5156-5163
8. 8 Snyder EE, Stormo GD ( 1995) Identification of protein coding regions in genomic DNA. J Mol Biol 248, 1-18
9. 9 Xu Y, Mural RJ, Uberbacher EC (1994) Constructing gene models from accurately predicted exons: an application of dynamic programming. Comput Applic Biosci 10, 613-623
10. 10 Borodovsky M, McIninch J (1993) GenMark: Parallel gene recognition for bothDNA strands. Computer Chem 17, 123-133
11. 11 Guigo R, Knudsen S, Drake N, Smith T (1992) Prediction of gene structure. J Mol Biol 226, 141-157
12. 12 Berget S (1995) Exon recognition in vertebrate splicing. J Biol Chem 270, 2411-2414
13. 13 Brunak S, Engelbrecht J, Knudsen S (1991) Prediction of human mRNA donor and acceptor sites from the DNA Sequence. J Mol Biol 220, 49-65
14. 14 Farber R, Lapedes A, Sirotkin K (1992) Determination of eucaryotic protein coding regions using neural networks and information theory. J Mol Biol 226, 471-479
15. 15 Mephu Nguifo E, Sallantin J (1993) Prediction of primate splice junction gene sequences with a cooperative knowledge acquisition system. Proceedings of 1st International Conference of Intelligent Systems for Molecular Biology. AAAI Press, Washington DC, USA, July 6-9, 292-300
16. 16 Huhns MN (ed) (1987) Distributed Artificial Intelligence. Morgan Kaufmann
17. 17 Savoure A, Jaoua S, Hua XJ, Ardiles W, Van Montagu M, Verbruggen N (1995) Isolation, characterization, and chromosomal location of a gene encoding the delta-pyrroline-5-carboxylate synthetase in Arabidopsis thaliana. FEBS Lett 372, 13-19
18. 18 Zhuang Y, Goldstein AM, Weiner, AM (1989) UACUAAC is the preferred branch site for mammalian mRNA splicing. Proc Natl Acad Sci USA 86, 2752-2756
19. 19 Smith CWJ, Chu TT, Nadal-Girard B (1993) Scanning and competition between AGs involved in 3′ splice site selection in mammalian introns. Mol Cell Biol 13, 4939-4952
20. 20 Seif I et al (1981) BKV splice sequences based on analysis of preferred donor and acceptor sites, Nucleic Acids Res 6, 3387-3398
21. 21 Penotti, FE (1991) Human Pre-mRNA splicing signals. J Theor Biol 150, 385-420
22. 22 Korning P, Hebsgaard S, Rouze P, Brunak S (1996) Cleaning the Genbank Arabidopsis thaliana data set. Nucleic Acids Res 24, 316-320
23. 23 Fickett JW, Tung CS (1992) Assessment of protein coding measures. Nucleic Acids Res 20, 6441-6450