Spectral distortion measures for biological sequence comparisons and database searching

Pattern Recognition

Volumn 40, Issue 2, 2007, Pages 516-529

  Pham, Tuan D ^a  

^a JAMES COOK UNIVERSITY   (Australia)

Author keywords

Bioinformatics; Distortion measures; DNA sequences; Protein sequences

Indexed keywords

ALGORITHMS; BIOLOGY; COMPUTATIONAL COMPLEXITY; COMPUTATIONAL METHODS; DNA SEQUENCES; GENES; PROTEINS;

BIOINFORMATICS; DISTORTION MEASURES; MOLECULAR MACHINES; PROTEIN SEQUENCES;

DATABASE SYSTEMS;

EID: 33750358065     PISSN: 00313203     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.patcog.2006.02.026     Document Type: Article

References (53)

1. Nagl S.B. Function prediction from protein sequence. In: Orengo C.A., Jones D.T., and Thornton J.M. (Eds). Bioinformatics: Genes, Proteins and Computers (2003), BIOS Scientific Publishers, Oxford, UK
2. Bishop M., and Rawlings C. Nucleic Acid and Protein Sequence Analysis-A Practical Approach (1987), IRL Press, Oxford
3. Ewens W.J., and Grant G.R. Statistical Methods in Bioinformatics (2001), Springer, NY
4. Miller W. Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics 17 (2001) 391-397
5. Krane D.E., and Raymer M.L. Fundamental Concepts of Bioinformatics (2003), Benjamin Cummings, San Francisco
6. Bellman R. Dynamic Programming (1957), Princeton University Press, Princeton, NJ
7. Needleman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (1970) 443-453
8. Smith T., and Waterman M. Identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195-197
9. Durbin R., Eddy S.R., Krogh A., and Mitchison G.J. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (1998), Cambridge University Press, Cambridge, UK
10. Asltschul S., Gish W., Miller W., Myers E., and LIPMAN D. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
11. Lipman D.J., and Pearson W.R. Rapid and sensitive protein similarity searches. Science 227 (1985) 1435-1441
12. Higgins D.G., and Sharp P.M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73 (1988) 237-244
13. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
14. Veljkovic V., Cosic I., Dimitrijevic B., and Lalovic D. Is it possible to analyze DNA and protein sequences by the methods of digital signal processing?. IEEE Trans. Biomed. Eng. 32 (1985) 337-341
15. Anatassiou D. Frequency-domain analysis of biomolecular sequences. Bioinformatics 16 (2000) 1073-1082
16. Lio P. Wavelets in bioinformatics and computational biology: state of art and perspectives. Bioinformatics 19 (2003) 2-9
17. Li L., Jin R., Kok P.L., and Wan W. Pseudo-periodic partitions of biological sequences. Bioinformatics 20 (2004) 295-306
18. del Carpio-Munoz C.A., and Carbajal J.C. Folding pattern recognition in proteins using spectral analysis methods. Genome Inform. 13 (2001) 163-172
19. Anatassiou D. Genomic signal processing. IEEE Signal Process. Mag. 18 (2001) 8-20
20. Vinga S., and Almeida J. Alignment-free sequence comparison-a review. Bioinformatics 19 (2003) 513-523
21. Blaisdell B.E. A measure of the similarity of sets of sequences not requiring sequence alignment. Proc. Natl. Acad. Sci. USA 83 (1986) 5155-5159
22. Wu T.J., Burke J.P., and Davison D.B. A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words. Biometrics 53 (1997) 1431-1439
23. Wu T.J., Hsieh Y.C., and Li L.A. Statistical measures of DNA dissimilarity under Markov chain models of base composition. Biometrics 57 (2001) 441-448
24. Stuart G.W., Moffett K., and Baker S. Integrated gene and species phylogenies from unaligned whole genome protein sequences. Bioinformatics 18 (2002) 100-108
25. 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 17 (2001) 149-154
26. Almeida J.S., Carrico J.A., Maretzek A., Noble P.A., and Fletcher M. Analysis of genomic sequences by chaos game representation. Bioinformatics 17 (2001) 429-437
27. Pham T.D., and Zuegg J. A probabilistic measure for alignment-free sequence comparison. Bioinformatics 20 (2004) 3455-3461
28. Cosic I. Macromolecular bioactivity: is it resonant interaction between macromolecules?-theory and applications. IEEE Trans. Biomed. Eng. 41 (1994) 1101-1114
29. Veljkovic V., and Slavic I. General model of pseudopotentials. Phys. Rev. Lett. 29 (1972) 105-108
30. Lazovic J. Selection of amino acid parameters for Fourier transform-based analysis of proteins. CABIOS 12 (1996) 553-562
31. de Trad C.H., Fang Q., and Cosic I. Protein sequence comparison based on the wavelet transform approach. Protein Eng. 15 (2002) 193-203
32. Daubechies I. The wavelet transform, time-frequency localization and signal analysis. IEEE Trans. Inform. Theory 36 (1990) 961-1005
33. Daubechies I. Where do wavelets come from?. Proceeding of the IEEE 84 (1996) 510-513 (Special Issue on Wavelets)
34. Tang Y.Y., Liu J., and Yang L.H. Wavelet Theory and its Application to Pattern Recognition (1999), World Scientific, Singapore
35. Q. Wu, K.R. Castleman, Automated chromosome classification using wavelet-based band pattern descriptors, Proceedings of 13th IEEE Symposium on Computer-Based Medical Systems, 2000, pp. 189-194.
36. Wang J.Z., Wiederhold G., Firschein O., and Wei S.X. Content-based image indexing and searching using Daubechies' wavelets. Int. J. Digital Libraries 1 (1998) 311-328
37. Hu Y., and Loizou P.C. Speech enhancement based on wavelet thresholding the multitaper spectrum. IEEE Trans. Speech Audio Process. 12 (2004) 59-67
38. Chen G.Y., and Bui T.D. Invariant fourier-wavelet descriptor for pattern recognition. Pattern Recognition 32 (1999) 1083-1088
39. Pirogova E., Simon G.P., and Cosic I. Investigation of the applicability of dielectic relaxation properties of amino acid solutions within the resonant recognition model. IEEE Trans. Nanobioscience 2 (2003) 63-69
40. Makhoul J. Linear prediction: a tutorial review. Proc. IEEE 63 (1975) 561-580
41. L. Rabiner, B.H. Juang, Fundamentals of Speech Recognition, Prentice-Hall, NJ, 1993.
42. V.K. Ingle, J.G. Proakis, Digital Signal Processing Using Matlab V.4, Boston, PWS Publishing, MA, 1997.
43. Gray R.M. Vector quantization. IEEE ASSP Mag. 1 (1984) 4-29
44. Itakura F., and Saito S. A statistical method for estimation of speech spectral density and formant frequencies. Electron. Commun. Japan 53A (1970) 36-43
45. J. Felsenstein, PHYLIP (Phylogeny Inference Package), version 3.5c. Distributed by the Author, Department of Genetics, University of Washington, Seattle, WA, 1993.
46. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16 (1980) 111-120
47. Jukes T.H., and Cantor C.R. Evolution of protein molecules. In: Munro H.N. (Ed). Mammalian Protein Metabolism (1969), Academic Press, NY 21-132
48. O'Shaughnessy D. Speech Communication-Human and Machine (1987), Addison-Wesley, Reading, MA
49. Lehninger A.L., Nelson D.L., and Cox M.M. Principles of Biochemistry (1993), Worth Publishing, New York
50. Epstein R.J. Human Molecular Biology: An Introduction to the Molecular Basis of Health and Disease (2003), Cambridge University Press, Cambridge
51. Mount D.W. Bioinformatics-Sequence and Genome Analysis. second ed. (2004), Cold Spring Harbor Laboratory Press, New York
52. Doolittle R. Similar amino acid sequences: chance or common ancestry?. Science 214 (1981) 149-159
53. Nocerino N., Soong F.K., Rabiner L.R., and Klatt D.H. Comparative study of several distortion measures for speech recognition. IEEE Proc. Int. Conf. Acoustics, Speech, and Signal Processing 11.4.1 (1985) 387-390