Thermodynamic modeling of donor splice site recognition in pre-mRNA

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 69, Issue 4 1, 2004, Pages

  Garland, Jeffrey A ^a   Aalberts, Daniel P ^a  

^a WILLIAMS COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; CHEMICAL BONDS; CORRELATION METHODS; ENTROPY; GENES; GENETIC ENGINEERING; MATRIX ALGEBRA; MOLECULES; PROBABILITY; THERMODYNAMICS;

BIOINFORMATICS; NUCLEOTIDES; THERMODYNAMIC MODELING; WEIGHT MATRIX METHOD (WMM);

RNA;

EID: 42749106244     PISSN: 15393755     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (26)

1. H. Lodish , Molecular Cell Biology, 4th ed. (W. H. Freeman, New York, 2000).
2. L. P. Lim and C. B. Burge, Proc. Natl. Acad. Sci. U.S.A. 98, 11 193 (2001).
3. Computational Methods in Molecular Biology, edited by S. L. Salzberg, D. B. Searls, and S. Kasif (Elsevier, Amsterdam, 1998).
4. R. Staden, Nucleic Acids Res. 12, 505 (1984).
5. F. S. Collins, , Nature (London) 422, 835 (2003).
6. Y-T. Yu , in The RNA World, Second Edition, edited by R. F. Gesteland, T. R. Cech, and J. F. Atkins (Cold Spring Harbor Lab. Press, Cold Spring Harbor, NY, 1999), pp. 487-524.
7. C. B. Burge, T. Tuschl, and P. A. Sharp, in The RNA World, Second Edition, edited by R. F. Gesteland, T. R. Cech, and J. F. Atkins (Cold Spring Harbor Lab. Press, Cold Spring Harbor, NY, 1999), pp. 525-560.
8. J. A. Wise, Science 262, 1978 (1993).
9. J. P. Staley and C. Guthrie, Cell 92, 315 (1998).
10. Z. Zhou , Nature (London) 419, 182 (2002).
11. D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner, J. Mol. Biol. 288, 911 (1999).
12. M. Zuker, D. H. Mathews, and D. H. Turner, in RNA Biochemistry Biotechnology, edited by J. Barciszewski and B. F. C. Clark (Kluwer, Dordrecht, 1999), pp. 11-43.
13. Other algorithms which calculate free energies for oligomeric associations include D. H. Mathews, RNA 5, 1458 (1999); M. Zuker, Nucleic Acids Res. 31, 3406 (2003); M. Andronescu , ibid. 31, 3416 (2003); N. O. Hodas and D. P. Aalberts (unpublished).
14. Other algorithms which calculate free energies for oligomeric associations include D. H. Mathews, RNA 5, 1458 (1999); M. Zuker, Nucleic Acids Res. 31, 3406 (2003); M. Andronescu , ibid. 31, 3416 (2003); N. O. Hodas and D. P. Aalberts (unpublished).
15. Other algorithms which calculate free energies for oligomeric associations include D. H. Mathews, RNA 5, 1458 (1999); M. Zuker, Nucleic Acids Res. 31, 3406 (2003); M. Andronescu , ibid. 31, 3416 (2003); N. O. Hodas and D. P. Aalberts (unpublished).
16. Other algorithms which calculate free energies for oligomeric associations include D. H. Mathews, RNA 5, 1458 (1999); M. Zuker, Nucleic Acids Res. 31, 3406 (2003); M. Andronescu , ibid. 31, 3416 (2003); N. O. Hodas and D. P. Aalberts (unpublished).
17. C. Burge and S. Karlin, J. Mol. Biol. 268, 78 (1997).
18. http://www.fruitfly.org/seq_tools/datasets/Human/GENIE_95/
19. The WMM is trained on the donor sites of the 380-gene Burge/Karlin learning set [14], calculating base-frequencies at positions starting three bases before and ending four bases after the consensus GU splice site.
20. M. Q. Zhang and T. G. Marr, CABIOS, Comput. Appl. Biosci. 9, 499 (1993).
21. Although many believe that the secondary structure of the pre-mRNA affects splicing, methods to predict splicing using this information have thus far had only limited success: D. J. Patterson, K. Yasuhara, and W. L. Ruzzo, in Pacific Symposium on Biocomputing 2002, eds. R. B. Altman, K. Dunker, L. Hunter, K. Lauderdale, and T. E. Klein (World Scientific, Singapore, 2002), pp. 223-234.
22. T. A. Brown, Genomes, 2nd ed. (Wiley, New York, 2002).
23. K. Ichiyanagi , Mol. Microbiol. 46, 1259 (2002).
24. J. Couzin, Science 298, 2296 (2002).
25. R. F. Ketting , Genes Dev. 15, 2654 (2001).
26. T. M. Lowe and S. R. Eddy, Science 283, 1168 (1999).