Sequence comparison via polar coordinates representation and curve tree

Journal of Theoretical Biology

Volumn 292, Issue , 2012, Pages 78-85

  Dai, Qi ^a   Guo, Xiaodong ^b   Li, Lihua ^b  

^a ZHEJIANG SCI TECH UNIVERSITY   (China)

^b HANGZHOU DIANZI UNIVERSITY   (China)

Author keywords

Curve matching distance; Graphical representation; Phylogenetic analysis; The closed curve

Indexed keywords

BETA GLOBIN;

BIOINFORMATICS; COMPARATIVE STUDY; GRAPHICAL METHOD; NUMERICAL METHOD; PHYLOGENETICS;

ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; CURVE FITTING; DNA SEQUENCE; EXON; HIGH THROUGHPUT SCREENING; HIGH THROUGHPUT SEQUENCING; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ANIMALS; BASE SEQUENCE; BETA-GLOBINS; CORONAVIRUS; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

EID: 80054085843     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.09.030     Document Type: Article

References (44)

1. Abo ElMaaty M.I., Abo-Elkhier M.M., AbdElwahaab M.A. 3D graphical representation of protein sequences and their statistical characterization. Physica A 2010, 389:4668-4676.
2. Bai F.L., Zhang J.H., Zheng J.S. Similarity analysis of DNA sequences based on the EMD method. Appl. Math. Lett. 2011, 24:232-237.
3. Chi R., Ding K.Q. Novel 4D numerical representation of DNA sequences. Chem. Phys. Lett. 2005, 407:63-67.
4. Durbin R., Eddy S.R., Krogh A., Mitchison G. Biological Sequence Analysis 1998, Cambridge University Press.
5. Felsenstein J. PHYLIP-Phylogeny inference package (version 3.2). Cladistics 1989, 5:164-166.
6. Gates M. A simple way to look at DNA. J. Theor. Biol. 1986, 119:319-328.
7. Gotoh O. An improved algorithm for matching biological sequences. J. Mol. Biol. 1982, 162:705-708.
8. Gu W., Zhou T., Ma J., Sun X., Lu Z. Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Res. 2004, 101:155-161.
9. Hamori E., Ruskin J. H-curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. J. Biol. Chem. 1983, 25:1318-1327.
10. Huang G.H., Liao B., Li Y.F., Yu Y.G. Similarity studies of DNA sequences based on a new 2D graphical representation. Biophys. Chem. 2009, 14:355-359.
11. Huang G.H., Zhou H.Q., Li Y.F., Xu L.X. Alignment free comparison of genome sequences by a new numerical characterization. J. Theor. Biol. 2011, 281:107-112.
12. Leong P.M., Morgenthaler S. Random walk and gap plots of DNA sequences. Comput. Appl. Biosci. 1995, 11:503-507.
13. Liao B., Ding K. A 3D graphical representation of DNA sequences and its application. Theor. Comput. Sci. 2006, 358:56-64.
14. Liu X.Q., Dai Q., Xiu Z.L., Wang T.M. PNN-curve: a new 2D graphical representation of DNA sequences and its application. J. Theor. Biol. 2006, 243:555-561.
15. Liao B., Wang T.M. Analysis of similarity/dissimilarity of DNA sequences based on 3-D graphical representation. Chem. Phys. Lett. 2004, 388:195-200.
16. Maaty M.A., Abo-Elkhier M.M., Elwahaab M.A.A. 3D graphical representation of protein sequences and their statistical characterization. Physica A 2010, 389:4668-4676.
17. Maaty M.A., Abo-Elkhier M.M., Elwahaab M.A.A. Representation of protein sequences on latitude-like circles and longitude-like semi-circles. Chem. Phys. Lett. 2010, 493:386-391.
18. Nandy A. A new graphical representation and analysis of DNA sequence structure: methodology and application to globin genes. Curr. Sci. 1994, 66:309-314.
19. Needleman S.B., Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970, 48:443-453.
20. Pham T.D., Zuegg J. A probabilistic measure for alignment-free sequence comparison. Bioinformatics 2004, 20:3455-3461.
21. Qi Z.H., Qi X.Q. Novel 2D graphical representation of DNA sequence based on dual nucleotides. Chem. Phys. Lett. 2007, 440:139-144.
22. Qi X.Q., Wen J., Qi Z.H. New 3D graphical representation of DNA sequence based on dual nucleotides. J. Theor. Biol. 2007, 249:681-690.
23. Randic M. Condensed representation of DNA primary sequences. J. Chem. Inf. Comput. Sci. 2000, 40:50-56.
24. Randic M., Vracko M. On the similarity of DNA primary sequences. J. Chem. Inf. Comput.Sci. 2000, 40:599-606.
25. Randic M., Guo X.F., Basak S.C. On the characterization of DNA primary sequence by triplet of nucleic acid bases. J. Chem. Inf. Comput. Sci. 2001, 41:619-626.
26. Randic M., Vracko M., Lers N., Plavsic O. Novel 2-D graphical representation of DNA sequences and their numerical characterization. Chem. Phys. Lett. 2003, 368:1-6.
27. Randic M., Vracko M., Lers N., Plavsic D. Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation. Chem. Phys. Lett. 2003, 371:202-207.
28. Randic M., Zupan J., Vikic-Topic D., Plavsic D. A novel unexpected use of a graphical representation of DNA: graphical alignment of DNA sequences. Chem. Phys. Lett. 2006, 431:375-379.
29. Randic M., Zupan J., Balaban A., Vikic-Topic D., Plavsic D. Graphical representation of proteins. Chem. Rev. 2011, 111:790-862.
30. Rota P.A., Oberste M.S., Monroe S.S., et al. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 2003, 300:1394.
31. Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981, 147:195-197.
32. Song J., Tang H. A new 2-D graphical representation of DNA sequences and their numerical characterization. J. Biochem. Biophys. Methods 2005, 63:228-239.
33. Vinga S., Almeida J. Alignment-free sequence comparison-a review. Bioinformatics 2003, 19:513-523.
34. Wang S.Y., Tian F.C., Qiu Y., Liu X. Bilateral similarity function: a novel and universal method for similarity analysis of biological sequences. J. Theor. Biol. 2010, 265:194-201.
35. Waterman M.S. Introduction to Computational Biology: Maps, Sequences, and Genomes: Interdisciplinary Statistics 1995, Chapman and Hall/CRC, Boca Raton, FL.
36. Wu Z.C., Xiao X., Chou K.C. 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.
37. Wen J., Zhang Y. A 2D graphical representation of protein sequence and its numerical characterization. Chem. Phys. Lett. 2009, 476:281-286.
38. Xie G.S., Mo Z.X. Three 3D graphical representations of DNA primary sequences based on the classifications of DNA bases and their applications. J. Theor. Biol. 2011, 269:123-130.
39. Yao Y.H., Wang T.M. A class of new 2-D graphical representation of DNA sequences and their application. Chem. Phys. Lett. 2004, 398:318-323.
40. Yao Y.H., Nan X.Y., Wang T.M. Analysis of similarity/dissimilarity of DNA sequences based on a 3-D graphical representation. Chem. Phys. Lett. 2005, 411:248-255.
41. Yu J.F., Sun X., Wang J.H. TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications. J. Theor. Biol. 2009, 261:459-468.
42. Zhang Z.J. DV-Curve: a novel intuitive tool for visualizing and analyzing DNA sequences. Bioinformatics 2009, 25:1112-1117.
43. Zhang Y.S., Chen W. Invariants of DNA sequences based on 2DD-curves. J. Theor. Biol. 2006, 242:382-388.
44. Zhang Y.S., Liao B. On the similarity of DNA sequences based on 3-D graphical representation. J. Biomath. 2007, 22:583-590.