Examining coding structure and redundancy in DNA

IEEE Engineering in Medicine and Biology Magazine

Volumn 25, Issue 1, 2005, Pages 62-68

  Rosen, Gail L ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

REPETITIVE DNA; DNA;

ARTICLE; DNA REPLICATION; DNA STRAND; DNA STRUCTURE; GENETIC CODE; MUTATION; TANDEM REPEAT; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; DNA DAMAGE; DNA REPAIR; GENETIC VARIABILITY; GENETICS; HUMAN; INFORMATION RETRIEVAL; INFORMATION SCIENCE; METHODOLOGY; SYSTEMS BIOLOGY;

ANIMALS; COMPUTATIONAL BIOLOGY; DNA; DNA DAMAGE; DNA REPAIR; GENETIC CODE; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INFORMATION THEORY; MODELS, GENETIC; SYSTEMS BIOLOGY; VARIATION (GENETICS);

EID: 33744971411     PISSN: 07395175     EISSN: None     Source Type: Journal    
DOI: 10.1109/MEMB.2006.1578665     Document Type: Article

References (32)

1. Y.K. Huen, "Brief comments on junk DNA: Is it really junk?" Complexity Int., vol. 9, pp. 1-12, 2002.
2. R.R. Sinden, V.N. Potaman, E.A. Oussatcheva, C.E. pearson, Y.L. Lyubchenko, and L.S. Shlyakhtenko, "Triplet repeat DNA structures and human genetic disease: Dynamic mutations from dynamic DNA," J. Biosci., vol. 27, no. 1, Feb. 2002.
3. N. Stambuk, "On circular coding properties of gene and protein sequences," Croatia Chemica Acta, vol. 72, no. 4, pp. 999-1008, 1999.
4. E.N. Trifonov, "3-, 10.5-, 200-, and 400-base periodcities in genome sequences," Physica A, vol. 249, no. 1-4, pp. 511-516, 1998.
5. B. Windle, "Telomerase: Target of immortality" [Online]. Available: http://www.people.vcu.edu/~bwindle/Telomerase/telomerase.html
6. W. Hahn. "Telomerase and cancer: Where and when?" Clinical Cancer Res., vol. 7, no. 10, pp. 2953-2954, Oct. 2001.
7. T.D. Schneider, G.D. Stormo, L. Gold, and A. Ehrenfeucht, "Information content of binding sites on nucleotide sequences," J. Mol. Biol., vol. 188, no. 3, pp. 415-431, 1986.
8. R.H. Burdon, Genes and the Environment. Philadelphia, PA: Taylor and Francis, 1999.
9. D. Metzgar, J. Bytof, and C. Wills, "Selection against frameshift mutations limits. Microsatellite expansion in coding DNA," Genome Res., vol. 10, no. 1, pp. 72-80, 2000.
10. D.A. Mac Donaill, "The role of error-coding in shaping the nucleotide alphabet: Nature's choice of A, U, C, and G," in Proc. IEEE EMBS Intl. Conf. Special Session Commun. Theory, Coding Theory Molecular Biol., pp. 3850-3853, 2003.
11. D. Anastassiou, "Genomic signal processing," IEEE Signal Processing Mag., pp 8-20, July 2001.
12. N. Chakravarthy, A. Spanias, L.D. Iasemidis, and K. Tsakalis, "Autoregressive modeling and feature analysis of DNA sequences," Eurasip Journal on Applied Signal Processing, vol. 1, pp. 13-28, 2004.〈
13. G.L. Rosen and J.D. Moore, "Investigation of coding structure in DNA," IEEE Int. Conf. Acoustics, Speech, Signal Processing (ICASSP), Apr. 2003.
14. "GeneMark: A family of gene prediction programs" [Online]. Available: http://opal.biology.gatech.edu/GeneMark/
15. S.B. Wicker, Error Control Systems. Upper Saddle River, NJ: Prentice Hall, 1995.
16. L.L. Gatlin, Information Theory and the Living System. New York: Columbia Univ. Press, 1972.
17. R. Ramon-Roldan, P. Bernaola-Galvan, and J.L. Oliver, "Application of information theory to DNA sequence analysis: A review," Pattern Recognition, vol. 29, no. 7, pp. 1187-1194, 1996.
18. T.D. Schneider, "Some lessons for molecular biology from information theory," Entropy Measures, Maximum Entropy Principle and Emerging Applications. New York: Springer-Verlag, 2003, pp. 229-237.
19. G. Battail, "Replication decoding revisitied," in Proc. IEEE Information Theory Workshop, Apr. 2003.
20. E.E. May, M.A. Vouk, D.L. Bitzer, and D.I. Rosnick, "An error-correcting code framework for genetic sequence analysis," J. Franklin Instit., vol. 341, no 1-2, pp. 89-109, Jan.-Mar. 2004.
21. E.E. May, M.A. Vouk, D.L. Bitzer, and D.I. Rosnick, "Coding theory based models for protein translation initiation in prokaryotic organisms," in Proc. Fifth Int. Workshop Information Processing Cells Tissues (IPCAT), 2003.
22. E.E. May, "Towards a biological coding theory discipline," New Thesis, vol. 1, no. 1, pp. 19-37, 2004.
23. D.C. Schmidt and E.E. May, "Visualizing ECC properties of E. coli K-12 translation initiation sites," in Proc. 2nd IEEE Workshop Genomic Signal Processing Statistics, 2004.
24. L.S. Liebovitch, Y. Tao, A.T. Todorov, and L. Levine, "Is there an error correcting code in the DNA?" Biophysical J., vol. 71, no. 3, pp. 1539-1544, 1996.
25. E.E. May, "Analysis of coding theory based models for initiating protein translation in prokaryotic organisms," Ph.D. dissertation, NC State Univ., 2002.
26. GenBank, "National Center for Biotechnology Database" [Online]. Available: http://www.ncbi.nlm.nih.gov
27. A. Hauth, "Identification of tandem repeats simple and complex pattern structures in DNA," Ph.D. dissertation, Univ. of Madison, WI, 2002.
28. M. Buchner and S. Janjarasjitt. "Detection and visualization of tandem repeats in DNA sequences," IEEE Trans. Signal Processing, vol. 51, no. 9, Sep. 2003.
29. R. Kolpakov, G. Bana, and G. Kucherov, "mreps Tandem Repeat Finder" [Online]. Available: http://www.loria.fr/mreps/.
30. G.L. Rosen, "Finding near-periodic DNA regions using a finite-field framework," in Proc. 2nd IEEE Workshop Genomic Signal Processing Stat., May 2004.
31. G.H. Golub and C.F. Van Loan, Matrix Computations, Baltimore, MD: Johns Hopkins Univ. Press, 1996.
32. A. Hauth [Online]. Available: http://www.cs.wisc.edu/gensoft/beyondTR/ static/HSVDJSAT.html