Identification of latent periodicity in amino acid sequences of protein families

Biochemistry (Moscow)

Volumn 71, Issue 1, 2006, Pages 18-31

  Turutina, V P ^a   Laskin, A A ^b   Kudryashov, N A ^b   Skryabin, K G ^a   Korotkov, E V ^a,b  

^a INSTITUTE OF BIOENGINEERING   (Russian Federation)

^b NATIONAL RESEARCH NUCLEAR UNIVERSITY MEPHI   (Russian Federation)

Author keywords

Alignment; Information decomposition; Latent periodicity

Indexed keywords

ALIGNMENT; MOLECULAR STRUCTURE; PROTEINS;

INFORMATION DECOMPOSITION; LATENT PERIODICITY; NOISE DECOMPOSITION;

AMINO ACIDS;

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGY; CHEMISTRY; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PROTEIN MOTIF; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 33644680693     PISSN: 00062979     EISSN: 16083040     Source Type: Journal    
DOI: 10.1134/S0006297906010032     Document Type: Article

References (37)

1. Ohno, S. (1970) Evolution by Gene Duplication, Springer-Verlag, Berlin.
2. Ohno, S., and Epplen, J. T. (1983) Proc. Natl. Acad. Sci. USA, 80, 3391-3395.
3. Ohno, S. (1984) J. Mol. Evol., 20, 313-321.
4. Heger, A., and Holm, L. (2000) Proteins, 41, 224-237.
5. Landau, G. M., Schmidt, J. P., and Sokol, D. (2001) J. Comp. Biol., 8, 1-18.
6. Neuwald, A. F., and Poleksic, A. (2000) Nucleic Acids Res., 28, 3570-3580.
7. Coward, E., and Drablos, F. (1998) Bioinformatics, 14, 498-507.
8. Katti, M. V., Sami-Subbu, R., Ranjekar, P. K., and Gupta, V. S. (2000) Protein Sci., 9, 1203-1209.
9. Andrade, M. A., Perez-Iratxeta, C., and Pouting, C. P. (2001) J. Struct. Biol., 134, 117-131.
10. Benson, G. (1999) Nucleic Acids Res., 27, 573-580.
11. Heringa, J. (1998) Curr. Opin. Struct. Biol, 8, 338-345.
12. Heringa, J., and Argos, P. (1993) Proteins, 17, 391-341.
13. Murray, K. B., Taylor, W. R., and Thornton, J. M. (2004) Proteins, 57, 365-380.
14. Rackovsky, S. (1998) Proc. Natl. Acad. Sci. USA, 95, 8580-8584.
15. McLachlan, A. D. (1993) J. Phys. Chem., 97, 3000-3006.
16. Jackson, J. H., George, R., and Herring, P. A. (2000) Biochem. Biophys. Res. Commun., 268, 289-292.
17. Makeev, V. J., and Tumanyan, V. G. (1996) Comput. Appl. Biosci., 12, 49-54.
18. Marcotte, E. M., Pellegrini, M., Yeates, T. O., and Eisenberg, D. (1999) J. Mol. Biol., 293, 151-160.
19. Andrade, M. A., Ponting, C. P., Gibson, T. J., and Bork, P. (2000) J. Mol. Biol., 298, 521-537.
20. Landschulz, W. H., Johnson, P. F., and McKnight, S. L. (1988) Science, 240, 1759-1764.
21. Korotkov, E. V., Korotkova, M. A., and Kudryashov, N. A. (2003) Phys. Lett. A, 312, 198-210.
22. Korotkov, E. V., Korotkova, M. A., and Kudryashov, N. A. (2003) Mol. Biol. (Moscow), 37, 436-451.
23. Korotkov, E. V., and Korotkova, M. A. (1996) DNA Res., 3, 157-167.
24. Laskin, A. A., Korotkov, E. V., Chaley, M. B., and Kudryashov, N. A. (2003) Mol. Biol. (Moscow), 37, 561-570.
25. Chaley, M. B., Korotkov, E. V., and Kudryashov, N. A. (2003) DNA Sequence, 14, 37-52.
26. Korotkov, E. V., and Korotkova, M. A. (2000) Mol. Biol. (Moscow), 34, 348-353.
27. Laskin, A. A., Korotkov, E. V., and Kudryashov, N. A. (2004) in Bioinformatics of Genome Regulation and Structure (Kolchanov, N. A., and Hofestaedt, R., eds.) Kluwer Press, New-York, pp. 135-144.
28. Holmes, I., and Durbin, R. (1998) J. Comput. Biol., 5, 493-504.
29. Henikoff, S., and Henikoff, J. G. (1993) Proteins, 17, 49-61.
30. Dodin, G., Vandergheynst, P., Levoir, P., Cordier, C., and Marcourt, L. (2000) J. Theor. iol., 206, 323-326.
31. Korotkova, M. A., Korotkov, E. V., and Rudenko, V. M. (1999) J. Mol. Model., 5, 103-115.
32. Chaley, M. B., Korotkov, E. V., and Skryabin, K. G. (1999) DNA Res., 6, 153-163.
33. Korotkov, E. V., Korotkova, M. A., and Tulko, J. S. (1997) CABIOS, 13, 37-44.
34. Kullback, S. (1959) Information Theory and Statistics, John Wiley & Sons, New-York.
35. George, R. A., and Heringa, J. (2000) Trends Biochem. Sci., 25, 515-517.
36. Bateman, A., Coin, L., Durbin, R., Finn, R. D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E. L. L., Studholme, D. J., Yeats, C., and Eddy, S. R. (2004) Nucleic Acids Res., 32, D138-D141.
37. Wolf, Y. I., Grishin, N. V., and Koonin, E. V. (2000) J. Mol. Biol., 299, 897-905.