Descriptors based on information theory for numerical characterization of DNA sequences

Current Science

Volumn 99, Issue 3, 2010, Pages 370-375

  Jayalakshmi, R ^a   Natarajan, R ^b,c   Vivekanandan, M ^d   Ganapathy Subramanian, N ^e  

^a BHARATHIDASAN UNIVERSITY   (India)

^b Centre for Mathematical Sciences   (India)

^c LAKEHEAD UNIVERSITY   (Canada)

^d Vivekanandha College of Arts and Sciences for Women   (India)

^e Texas Tech University   (United States)

Author keywords

globin genes; Alignment free sequence comparison; DNA descriptors; Information theory; Numerical characterization; Phylogenetic analysis

Indexed keywords

EID: 77956205320     PISSN: 00113891     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (24)

1. Shannon, C. E., A mathematical theory of communication. Bell. Syst. Tech. J., 1948, 27, 379-423.
2. Cosmi, C., Cuomo, V., Ragosta, M. and Macchiato, M. F., Characterization of nucleotidic sequences using maximum entropy techniques. J. Theor. Biol., 1990, 147, 423-432.
3. Frappat, L., Minichini, C., Sciarrino, A. and Sorba, P., Universality and Shannon entropy of codon usage. Phys. Rev. E., 2003, 68, 061910.
4. Ragosta, M., Cosmi, C., Cuomo, V. and Macchiato, M., An application of maximum entropy techniques to determine homogeneous sets of nucleotidic sequences. J. Theor. Biol., 1992, 155, 129-136.
5. Steinbach, P. J., Two-dimensional distributions of activation enthalpy and entropy from kinetics by the maximum entropy method. Biophys. J., 1996, 70, 1521-1528.
6. Mantegna, R. N., Buldyrev, S. V., Goldberger, A. L., Havlin, S., Peng, C. K., Simons, M. and Stanley, H. E., Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics. Phys. Rev. E, 1995, 52, 2939-2950.
7. Dehnert, M., Helm, W. E. and Hntt, M. T., Information theory reveals large-scale synchronisation of statistical correlations in eukaryote genomes. Gene, 2005, 345, 81-90.
8. García, J. A., Alvarez, S., Flores, A., Govezensky, T., Bobadilla, J. R. and José, M. V., Statistical analysis of the distribution of amino acids in Borrelia burgdorferi genome under different genetic codes. Physica A, 2004, 342, 288-293.
9. Holste, D., Grosse, I., Beirer, S., Schieg, P. and Herzel, H., Repeats and correlations in human DNA sequences. Phys. Rev. E, 2003, 67, 061913.
10. Li, C. and Wang, J., Relative entropy of DNA and its application. Physica A, 2005, 347, 465-471.
11. Li, M., Badger, J. H., Chen, X., Kwong, S., Kearney, P. and Zhang, H., An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics, 2001, 17, 149-154.
12. Schneider, T. D., Stormo, G. D., Gold, L. and Ehrenfeucht, A., Information content of binding sites on nucleotide sequences. J. Mol. Biol., 1986, 188, 415-431.
13. Nandy, A., Investigations on evolutionary changes in base distributions in gene sequences. Internet J. Mol. Design, 2002, 1, 545-548.
14. Blaisdell, B. E., A measure of the similarity of sets of sequences not requiring sequence alignment. Proc. Natl. Acad. Sci. USA, 1986, 83, 5155-5159.
15. Blaisdell, B. E., Average values of dissimilarity measure not requiring sequence alignment are twice the averages of conventional mismatch counts requiring sequence alignment for a computer-generated model system. J. Mol. Evol., 1989, 29, 538-547.
16. Blaisdell, B. E., Effectiveness of measures requiring and not requiring prior sequence alignment for estimating the dissimilarity of natural sequences. J. Mol. Evol., 1989, 29, 526-537.
17. Almeida, J. S. and Vinga, S., Alignment-free sequence comparison - a review. Bioinformatics, 2003, 19, 513-523.
18. Qi, J., Luo, H. and Hao, B., CVTree: a phylogenetic tree construction tool based on whole genomes. Nucleic Acids Res., 2004, 32, W45-W47.
19. Qi, J., Wang, B. and Hao, B., Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J. Mol. Evol., 2004, 58, 1-11.
20. Chu, K. H., Qi, J., You, Z. and Anh, V., Origin and phylogeny of chloroplast revealed by a simple correlation analysis of complete genomes. Mol. Biol. Evol., 2004, 21, 200-206.
21. Basak, S. C., Information theoretic indices of neighborhood complexity and their applications. In Topological Indices and Related Descriptors in QSAR and QSPR (eds Devillers, J. and Balaban, A. T.), Gordon and Breach Science, The Netherlands, 1999, pp. 563-593.
22. Nandy, A., Harle, M. and Basak, S. C., Mathematical descriptors of DNA sequences: development and applications. ARKIVOC, 2006, ix, 211-238.
23. Zupan, J. and Randić, M., Algorithm for coding DNA sequences into 'spectrum-like' and 'zigzag' representations. J. Chem. Inf. Model., 2005, 45, 309-313.
24. Ghosh, A., Nandy, A., Nandy, P., Gute, B. D. and Subhash Basak S. C., Computational study of dispersion and extent of mutated and duplicated sequences of the H5N1 influenza neuraminidase over the period 1997-2008. J. Chem. Inf. Model., 2009, 49, 2627-2638