Prediction of eukaryotic mRNA translational properties

Bioinformatics

Volumn 15, Issue 7-8, 1999, Pages 704-712

  Kochetov, Alex V ^a   Ponomarenko, Mikhail P ^a   Frolov, Anatoly S ^a   Kisselev, Lev L ^b   Kolchanov, Nikolay A ^a  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; POLYPEPTIDE;

CONFERENCE PAPER; DATA BASE; EUKARYOTE; GENE EXPRESSION; MAMMAL; NUCLEOTIDE SEQUENCE; PLANT; PREDICTION; PRIORITY JOURNAL; RNA SEQUENCE; RNA TRANSLATION;

EUKARYOTA; MAMMALIA;

EID: 0032844392     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.7.704     Document Type: Conference Paper

References (29)

1. Brown, C.M., Stockwell, P.A., Trotman, C.N.A. and Tate, W.P. (1990) Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes. Nucleic Acids Res., 18, 6339-6345.
2. Chen, C.-Y.A. and Shyu, A.-B. (1995) AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem. Sci., 20, 465-170.
3. Etzold, T. and Argos, P. (1993) SRS - an indexing and retrieval tool for flat file data libraries. Comput. Appl. Biosci., 9, 49-57.
4. Fishburn, P.C. (1970) Utility Theory for Decision Making. John Wiley & Sons, New York.
5. Futterer, J. and Hohn, T. (1992) Role of an upstream open reading frame in the translation of polycistronic mRNAs in plant cells. Nucleic Acids Res., 20, 3851-3857.
6. Futterer, J. and Hohn, T. (1996) Translation in plants - rules and exceptions. Plant Mol. Biol., 32, 159-189.
7. Gallie, D.R (1996) Translational control of cellular and viral mRNAs. Plant Mol. Biol., 32, 145-158.
8. Gallie, D.R. and Walbot, V. (1992) Identification of the motifs within the tobacco mosaic virus 5′-leader responsible for enhancing translation. Nucleic Acids Res., 20, 4631-4638.
9. Gallie, D.R., Sleat, D.E., Watts, J.W., Turner, P.C. and Wilson, T.M. (1987) The 5′-leader sequence of tobacco mosaic virus RNA enhances the expression of foreign gene transcripts in vitro and in vivo. Nucleic Acids Res., 15,:3257-3273.
10. Ikemura, T. (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol., 2, 13-34.
11. Ischenko, I.V., Kochetov, A.V., Kel, A.E., Kisselev, L.L. and Kolchanov, N.A. (1996) Comparative analysis of the local secondary structure of mRNAs encoded by high and low-expression eukaryotic genes. In Computer Science and Biology. Proceeding of the German Conference on Bioinformatics, Leipzig, pp. 124-129.
12. Jobling, S.A. and Gehrke, L (1987) Enhanced translation of chimaeric messenger RNAs containing a plant viral untranslated leader sequence. Nature, 325, 622-625.
13. Kel, A.E., Ponomarenko, M.P., Likhachev, E.A., Orlov, Y.L., Ischenko, J.V., Milanesi, L. and Kolchanov, N.A. (1993) SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. Comput. Appl. Biosci., 9, 617-627.
14. Kendall, M. and Gibbons, J.D. (1990) Rank Correlation Methods, 5th edn. Edward Arnold, London.
15. Kochetov, A.V., Ponomarenko, M.P., Vorobiev, D.G., Frolov, A.S., Kisselev, L.L. and Kolchanov, N.A. (1998a) Eukaryotic mRNAs encoding abundant and scarce proteins are dissimilar in many structural features of 5′-untranslated leaders. In Kolchanov, N.A. et al. (eds), Proceedings of the 1st International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, 1, pp. 214-217.
16. Kochetov, A.V., Pilugin, M.V., Kolpakov, F.A., Babenko, V.N., Kvashnina, E.V. and Shumny, V.K. (1998b) Structural and compositional features of 5′ untranslated regions of higher plant mRNAs. In Kolchanov, N.A. et al. (eds), Proceedings of the 1st International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, 1, pp. 210-213.
17. Kochetov, A.V., Ischenko, I.V., Vorobiev, D.G., Kel, A.E., Babenko, V.N., Kisselev, L.L. and Kolchanov, N.A. (1998c) Eukaryotic mRNAs encoding abundant and scarce proteins are statistically dissimilar in many structural features. FEBS Lett., 440, 351-355.
18. Kolchanov, N.A. et al. (1998) GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences of the eukaryotic genome. In Glasgow, J. et al. (eds), Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, ISMB-98, Montreal, Canada. AAAI Press, Menlo Park, CA, pp. 95-104.
19. Kozak, M. (1986) Bifunctional messenger RNAs in eukaryotes. Cell, 47, 481-483.
20. Kozak, M. (1987) At least 6 nucleotides preceding the AUG initiator codon enhance translation in mammalian cells. J. Mol. Biol., 196, 947-950.
21. Kozak, M. (1994) Determinants of translational fidelity and efficiency in vertebrate mRNAs. Biochimie, 76, 815-821.
22. Likhoshvai, V.A. and Matushkin, Yu.G. (1998) Theoretical analysis of possible evolutionary trends in codon distribution along the mRNA. In Kolchanov, N.A. et al. (eds), Proceedings of the 1st International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, 2, pp. 341-344.
23. Pahl, H.L. and Baeuerle, P.A. (1996) Control of gene expression by proteolysis. Curr. Opin. Cell Biol., 8, 340-347.
24. Pain, V. (1996) Initiation of protein synthesis in eukaryotic cells. Eur. J. Biochem., 236, 747-771.
25. Ponomarenko, M.P., Kolchanova, A.N. and Kolchanov, N.A. (1997) Generating programs for predicting the activity of functional sites. J. Comput. Biol., 4, 83-90.
26. Ponomarenko, M.P., Frolov, A.S., Ponomarenko, J.V., Podkolodnaya, O.A., Vorobyev, D.V., Kolchanov, N.A. and Overton, G.C. (1998) Mean-recognition: a systematic approach increasing the accuracy of the functional site recognition for the genomic DNA annotation. In Callaos, N. and Holmes, L. (eds), Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics, SCI'98, Vol. 4, IIIS, Orlando, FL, pp. 224-230.
27. Rao, C.D., Pech, M., Robbins, K.C. and Aaronson, S.A. (1988) The 5′ untranslated sequence of the c-sis/platelet-derived growth factor 2 transcript is a potent translational inhibitor. Mol. Cell. Biol., 8, 284-292.
28. Ray, B.K., Brendler, T.G., Adya, S., Daniels-McQeen, S., Miller, J.K., Hershey, J.W.B., Grifo, J.A., Merrick, W.C. and Thach, R.E. (1983) Role of mRNA competition in regulating translation: further characterization of mRNA discriminatory initiation factors. Proc. Natl Acad. Sci. USA, 80, 663-667.
29. Wingender, E., Dietze, P., Karas, H. and Knueppel, R. (1996) TRANS-FAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res., 24, 238-241.