W-curve alignments for HIV-1 genomic comparisons

PLoS ONE

Volumn 5, Issue 6, 2010, Pages

  Cork, Douglas J ^a,b,c   Lembark, Steven ^d   Tovanabutra, Sodsai ^a,b   Robb, Merlin L ^a,e   Kim, Jerome H ^a,e  

^a United States Military HIV Research Program   (United States)

^b HENRY M JACKSON FOUNDATION FOR THE ADVANCEMENT OF MILITARY MEDICINE   (United States)

^c ILLINOIS INSTITUTE OF TECHNOLOGY   (United States)

^d Workhorse Computing   (United States)

^e WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEIN GP 120;

ALGORITHM; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; FEMALE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; INTERMETHOD COMPARISON; NEWBORN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; UNINDEXED SEQUENCE; VIRUS GENOME;

ALGORITHMS; DNA, VIRAL; GENOME, VIRAL; HIV-1; RNA, VIRAL;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 77955218411     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010829     Document Type: Article

References (30)

1. Wu D, Roberge J, Cork DJ, Nguyen BG, Grace T (1993) Computer visualization of long genomic sequences, in Visualization 1993, IEEE Press, New York City, New York, CP 33: 308-315.
2. Jeffrey HJ (1990) Chaos game representation of gene structure. Nucleic Acids Res 18: 2163-2170.
3. Almeida JS, Carrico JA, Maretzek A, Noble PA, Fletcher M (2001) Analysis of genomic sequences by chaos game representation. Bioinformatics 17(5): 429-437.
4. Huang G, Liao B, Li Y, Yu Y (2009) Similarity studies of DNA sequences based on a new 2D graphical representation. Biophysical Chem 143: 55-59.
5. Cork DJ, Marland E, Zmuda J, Hutch TB (2002) Achieving Congruency of Phylogenetic Trees Generated by W-curves of Genomic Sequences. In: FValafar, ed. Techniques in Bioinformatics and Medical Informatics. Part I. Bioinformatics. Ann. N. Y. Acad. Sci Volume 980: 32-40.
6. Cork DJ (2003) Achieving Consensus of Long Genomic Sequences with the Wcurve. In: Lapointe FJ, McMorris FR, Janowitz MF, Mirkin B, Roberts FS, eds; Bioconsensus. DIMACS Series in Discrete Mathematics and Theoretical Computer Science 61:123-134; American Mathematical Society, Providence, R.I.
7. Cork DJ, Wu D, North MJ (2008) Geometric global genomic informatics for RNA viruses, Int. J. Medical Engineering and Informatics 1: 227-249.
8. Cork DJ, Toguem A (2002) Using Fuzzy Logic to Confirm the Integrity of a Pattern Recognition Algorithm for Long Genomic Sequences: The W-curve. In: Valafar F, ed. Techniques in Bioinformatics and Medical Informatics. Part I. Bioinformatics. Ann. N. Y. Acad. Sci, Volume 980: 32-40.
9. Basu S, Pan A, Dutta C, Das J (1992) Mathematical characterization of chaos game representation. New algorithms for nucleotide sequence analysis. J Mol Biol 228: 715-719.
10. http://mypages.iit.edu/cork/houstep/introduction.
11. http://www.bioinformatics.org/wcurve/.
12. Hill KA, Schisler NJ, Singh SM (1992) Chaos game representation of coding regions of human globin genes and alcohol dehydrogenase genes of phylogenetically divergent species. J Mol Evol 35: 261-269.
13. Oliver JL, Bernaola-Galvan P, Guerrero G, Roman-Roldan R (1993) Entropic profiles of DNA sequences through chaos-game-derived images. J Theor Biol 160(4): 457-470.
14. Deschavanne PJ, Giron A, Vilain J, Fagot G, Fertil B (1999) Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol Biol Evol 16(10): 1391-1399.
15. Joseph J, Sasikumar R (2006) Chaos game representation for comparison of whole genomes. BMC Bioinformatics 7: 243.
16. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F (1997) The Clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876-82.
17. Tovanabutra S, de Souza M, Sittisombut N, Sriplienchan S, Ketsararat V, et al. (2007) HIV-1 genetic diversity and compartmentalization in mother/infant pairs infected with CRF-1_AE. AIDS 21, No.8: 1050-1053.
18. Felsenstein J (1992) PHYLIP (Phylogeny Inference package), 3.5c and 3.67 eds. Department of Genetics, University of Washington, Seattle, WA.
19. Wang Y, Hill K, Singh S, Kari L (2005) The spectrum of genomic signatures: from dinucleotides to chaos game representation. Gene 346: 173-185.
20. Yu ZG, Anh V, Lau KS (2005) Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses. Journal of Theoretical Biology 226: 341-348.
21. Feng J, Wang T (2008) A 3D graphical representation of RNA secondary structures based on chaos game representation. Chemical Physical Letters 454: 355-361.
22. Fenyö EM, Heath A, Dispinseri S, Holmes H, Lusso P, et al. (2009) International network for comparison of HIV neutralization assays: The NeutNet report. PLoS ONE 4(2): e4505.
23. Brown BK, Sanders-Buell E, Rosa Borges A, Robb ML, Birx DL, et al. (2008) Cross-clade neutralization patterns among HIV-1 strains from the six major clades of the pandemic evaluated and compared in two different models. Virology 375: 529-538.
24. Scarlatti G, Albert J, Rossi P, Hodara V, Biraghi P, et al. (1993) Mother-to-child transmission of human immunodeficiency virus type 1: correlation with neutralizing antibodies against primary isolates. J Infect Dis 168: 207-210.
25. Polonis VR, Chanbancherd P, Chantakulkij S, Jugsudee A, Loomis-Price LD, et al. (2001) HIV type 1 subtype E-infected patients with broadened, dual (B/E) V3 loop serology have increased cross-neutralizing antibodies. AIDS Res Hum Retroviruses 17: 69-79.
26. Mascola J, Gilbert P, Hahn BH, Haigwood NL, Morris L, et al. (2005) Recommendations for the design and use of standard virus panels to assess neutralizing antibody responses elicited by candidate human immunodeficiency virus type 1 vaccines. J Virol 79: 10103-10107.
27. Nyambi PN, Nkengasong J, Lewi P, Andries K, Janssens W, et al. (1996) Multivariate analysis of human immunodeficiency virus type 1 neutralization data. J Virol 70: 6235-6243.
28. Peitgen HO, Jurgens H, Saupe D (1992) Chaos and Fractals: New Frontiers of Science. Springer Verlag, New York.
29. Barnsley MF (1988) Fractals Everywhere. Academic Press, San Diego.
30. Mandelbrot BB (2004) Fractal Geometry of Nature. H.B. Fenn and Company, Ltd., Canada.