Phylogenetic analysis of DNA sequences based on the generalized pseudo-amino acid composition

Journal of Theoretical Biology

Volumn 269, Issue 1, 2011, Pages 217-223

  Huang, Yujuan ^a,b   Yang, Lianping ^a,c   Wang, Tianming ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^b SHANDONG JIAOTONG UNIVERSITY   (China)

^c NORTHEASTERN UNIVERSITY   (China)

Author keywords

Dinucleotide; DNA; LZ complexity; Phylogenetic tree

Indexed keywords

DINUCLEOTIDE; DNA;

AMINO ACID; DNA; GENETIC ANALYSIS; PHYLOGENETICS; VECTOR;

AMINO ACID COMPOSITION; ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; MATHEMATICAL ANALYSIS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL;

AMINO ACIDS; ANIMALS; BASE SEQUENCE; DATABASES, NUCLEIC ACID; DNA; HEPATITIS E VIRUS; MAMMALS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 78149354443     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.10.027     Document Type: Article

References (53)

1. Andraos J. Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws: new methods based on directed graphs. Can. J. Chem. 2008, 86:342-357.
2. Berger J., Mitra S., Carli M., Neri A. Visualization and analysis of DNA sequences using DNA walks. J. Franklin I 2004, 341:37-53.
3. Blaisdell B. A measure of the similarity of sets of sequences not requiring sequence alignment. Proc. Natl. Acad. Sci. USA 1986, 83:5155-5159.
4. Chou K.C. Graphical rules in steady and non-steady enzyme kinetics. J. Biol. Chem. 1989, 264:12074-12079.
5. Chou K. Review: applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems. Biophys. Chem. 1990, 35:1-24.
6. Chou K., Zhang C. Diagrammatization of codon usage in 339 HIV proteins and its biological implication. AIDS Res. Hum. Retrov. 1992, 8:1967-1976.
7. Chou K. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins Struct. Funct. Genet. 1995, 21:319-344.
8. Chou K., Zhang C. Review: prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol. 1995, 30:275-349.
9. Chou K., Zhang C., Elrod D. Do antisense proteins exist?. J. Prot. Chem. 1996, 15:59-61.
10. Chou K. Prediction of protein cellular attributes using pseudo amino acid composition. Proteins Struct. Funct. Genet. 2001, 43:246-255.
11. Chou K. Review: structural bioinformatics and its impact to biomedical science. Curr. Med. Chem. 2004, 11:2105-2134.
12. Chou K. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics 2005, 21:10-19.
13. Chou K., Shen H. Review: recent progresses in protein subcellular location prediction. Anal. Biochem. 2007, 370:1-16.
14. Chou K., Shen H. Cell-PLoc: a package of web-servers for predicting subcellular localization of proteins in various organisms. Nat. Protocols 2008, 3:153-162.
15. Dai Q., Wang T. Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison. Bioinformatics 2008, 24:2296-2302.
16. Ding S., Dai Q., Liu H., Wang T. A simple feature representation vector for phylogenetic analysis of DNA sequences. J. Theor. Biol. 2010, 265:618-623.
17. Durbin R., Eddy S., Krogh A., Mitchison G. Biological Sequence Analysis 1998, Cambridge University Press, Cambridge, New York.
18. Felsensein J. Phylip-phylogeny inference package (version 3.2). Cladistics 1989, 5:164-166.
19. Grumbach S., Tahi F. Compression of DNA Sequences. In Data Compression Conference 1993, IEEE Computer Society Press, Sbowbird, Utah, USA.
20. Grumbach S., Tahi F. A new challenge for compression algorithms: genetic sequence. J. Info. Proc. Man. 1994, 30:866-875.
21. Huang G., Liao B., Li Y., Yu Y. Similarity studies of DNA sequences based on a new 2d graphical representation. Biophys. Chem. 2009, 143:55-59.
22. Li C., Wang J. Similarity analysis of DNA sequences based on the generalized LZ complexity of (0,1)-sequences. J. Math. Chem. 2006, 43(1):26-31. Preprint.
23. Li C., Yu X., Yang L., Zheng X., Wang Z. 3-D maps and coupling numbers for protein sequences. Phys. A 2009, 388:1967-1972.
24. Liao B. A 2-D graphical representation of DNA sequence. Chem. Phys. Lett. 2005, 401:196-199.
25. Liao B., Wang T. Analysis of similarity/dissimilarity of DNA sequences based on 3-d graphical representation. Chem. Phys. Lett. 2004, 388(1-3):195-200.
26. Liu Z., Meng J., Sun X. A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping. Biochem. Biophys. Res. Commun. 2008, 368:223-230.
27. Myers D., Palmer G. Microcomputer tools for steady-state enzyme kinetics. Bioinformatics 1985, 1:105-110.
28. Nandy A., Nandy P. On the uniqueness of quantitative DNA difference descriptors in 2D graphical representation models. Chem. Phys. Lett. 2003, 368:102-107.
29. Otu H., Sayood K. A new sequence distance measure for phylogenetic tree construction. Bioinformatics 2003, 19:2122-2130.
30. Qi X., Wen J., Qi Z. New 3-D graphical representation of DNA sequence based on dual nucleotides. J. Theor. Biol. 2007, 249:681-690.
31. Randic M., Balaban A. On a four-dimensional representation of DNA primary sequences. J. Chem. Inf. Comput. Sci. 2003, 43:532-539.
32. Randic M., Vracko M. On the similarity of DNA primary sequences. J. Chem. Inf. Comput. Sci. 2000, 40:599-606.
33. Randic M., Vracko M., Lers N., Plavsic D. Novel 2-D graphical representation of DNA sequences and their numerical characterization. Chem. Phys. Lett. 2003, 368:1-6.
34. Reinert G., Schbath S., Waterman M. Probabilistic and statistical properties of words: an overview. J. Comput. Biol. 2000, 7:1-46.
35. Robinson D., Foulds L. Comparison of phylogenetic trees. Math. Biosci. 1981, 53:131-147.
36. Vinga S., Almeida J. Alignment-free sequence comparison-a review. Bioinformatics 2003, 19:513-523.
37. Waterman M. Introduction to Computational Biology: Maps, Sequences, and Genomes 1995, Chapman & Hall, New York.
38. Wu T., Burke J., Davison D. A measure of DNA sequence dissimilarity based on mahalanobis distance between frequencies of words. Biometrics 1997, 53:1431-1439.
39. Wu T., Hsieh Y., Li L. Statistical measures of DNA dissimilarity under Markov chain models of base composition. Biometrics 2001, 57:441-448.
40. Wu Z., Xiao X., Chou K. 2D-MH: a web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids. J. Theor. Biol. 2010, 267:29-34.
41. Xiao X., Shao S., Ding Y., Chen X. Digital coding for amino acid based on cellular automata. IEEE Int. Conf. Syst. Man and Cybern. 2004, 5:4593-4598.
42. Yang L., Zhang X., Wang T. The Burrows-Wheeler similarity distribution between biological sequences based on Burrows-Wheeler transform. J. Theor. Biol. 2010, 262:742-749.
43. Yang L., Chang G., Zhang X., Wang T. Use of the Burrows-Wheeler similarity distribution to the comparison of the proteins. Amino Acids 2010, 39:887-898.
44. Yao Y., Nan X., Wang T. Analysis of similarity/dissimilarity of DNA sequences based on a 3-D graphical representation. Chem. Phys. Lett. 2005, 411:248-255.
45. Yao Y., Wang T. A class of new 2-D graphical representation of DNA sequences and their application. Chem. Phys. Lett. 2004, 398:318-323.
46. Zheng X., Qin Y., Wang J. A complexity-based measure and its application. J. Math. Chem. 2009, 46:1149-1157.
47. Zhang C., Chou K. Analysis of codon usage in 1562 E.Coli protein coding sequences. J. Mol. Biol. 1994, 238:1-8.
48. Zhang S., Wang T. Phylogenetic analysis of protein sequences based on conditional LZ complexity. MATCH Commun. Math. Comput. Chem. 2010, 63(3):701-716.
49. Zhang S., Wang T. A complexity-based method to compare RNA secondary structures and its application. J. Biomol. Struct. Dyn. 2010, 28(2):247-258.
50. Zhang Y., Tan M. Visualization of DNA sequences based on 3DD-Curves. J. Math. Chem. 2008, 44(1):206-216.
51. Zhou G., Deng M. An extension of Chous graphical rules for deriving enzyme kinetic equations to system involving parallel reaction pathways. Biochem. J. 1984, 222:169-176.
52. Ziv J., Lempel A. A universal algorithm for sequential data compression. IEEE Trans. Inf. Theory 1977, 23:337-343.
53. Ziv, J., Lempel, A., 1978. Compression of individual sequences by variable rate coding, IEEE Trans. Inf. Theory, USA, pp. 530-536.