Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Zaslavsky, Leonid ^a   Bao, Yiming ^a   Tatusova, Tatiana A ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXPLORATORY ANALYSIS; GEOGRAPHIC LOCATION; SEASONAL DISTRIBUTIONS; SEQUENCE SIMILARITY; STRUCTURED METADATAS; SYSTEMATIC SAMPLING; TREE REPRESENTATION; VISUALIZATION TOOLS;

TREES (MATHEMATICS); VISUALIZATION;

AGGREGATES;

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC DATABASE; GENETIC SIMILARITY; GEOGRAPHIC DISTRIBUTION; INFLUENZA VIRUS; MATHEMATICAL ANALYSIS; NONHUMAN; PHYLOGENETIC TREE; SAMPLING; SEASONAL VARIATION; SEQUENCE ANALYSIS; TAXONOMIC RANK; VIRUS GENE; WEB BROWSER; ALGORITHM; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER GRAPHICS; COMPUTER SIMULATION; DNA SEQUENCE; GENETICS; METHODOLOGY; ORTHOMYXOVIRUS; SAMPLE SIZE; VIRUS GENOME;

ORTHOMYXOVIRIDAE;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTER GRAPHICS; COMPUTER SIMULATION; GENOME, VIRAL; MODELS, GENETIC; ORTHOMYXOVIRIDAE; SAMPLE SIZE; SEQUENCE ANALYSIS, DNA; USER-COMPUTER INTERFACE;

EID: 44849127354     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-237     Document Type: Article

References (25)

1. The NCBI Influenza Virus Resource http://www.ncbi.nlm.nih.gov/genomes/FLU
2. Fauci AS Race against time Nature 2005, 435(7041):423-424. 10.1038/ 435423a 15917781
3. Ghedin E Sengamalay NA Shumway M Zaborsky J Feldblyum T Subbu V Spiro DJ Sitz J Koo H Bolotov P Dernovoy D Tatusova T Bao Y St George K Taylor J Lipman DJ Fraser CM Taubenberger JK Salzberg SL Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution Nature 2005, 437(7062):1162-1166. 10.1038/nature04239 16208317
4. Bao Y Bolotov P Dernovoy D Kiryutin B Zaslavsky L Tatusova T Ostell J Lipman D The Influenza Virus Resource at the National Center for Biotechnology Information Journal of Virology 2008, 82(2):596-601. 2224563 17942553 10.1128/JVI.02005-07
5. Mather G Foundations of Perception Psychology Press 1 2006
6. Baron J Thinking and Deciding Cambridge University Press 3 2000
7. Card SKND Degree-of-interest trees: A component of an attention-reactive user interface Proc Advanced Visual Interfaces (AVI) 2002:231-245.
8. Fekete J-DPC Interactive information visualization of a million items Proc InfoVis 2002:117-124.
9. Lamping JPP Rao R Focus+Content Technique Based on Hyperbolic Geometry for Viewing Large Hierarchies Proc CHI'95 1995:401-408.
10. Rost U Bornberg-Bauer E Treewiz: Interactive exploration of huge trees Bioinformatics 2002, 18:109-114. 10.1093/bioinformatics/18.1.109 11836218
11. Beermann D Munznerz T Humphreysy G Scalable, Robust Visualization of Very Large Trees EUROGRAPHICS - IEEE VGTC Symposium on Visualization Brodlie KW, Duke KIJDJ 2005, :1-8.
12. Dufayard JF Duret L Penel S Gouy M Rechenmann F Perriere G Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence databases Bioinformatics 2005, 21:2596-2603. 10.1093/bioinformatics/bti325 15713731
13. Chevenet F Brun C Banuls AL Jacq B Christen R TreeDyn: Towards dynamic graphics and annotations for analyses of trees BMC Bioinformatics 2006, 7:439. 1615880 17032440 10.1186/1471-2105-7-439
14. Kramer J Is abstraction the key to computing? ACM Communications 2007, 50(4):36-42. 10.1145/1232743.1232745
15. PhyloWidget, a program for viewing, editing, and publishing phylogenetic trees online http://www.phylowidget.org
16. MacEachren AM How Maps Work: Representation, Visualization, and Design. 2nd revised edition The Guilford Press 2004
17. Zaslavsky L Bao Y Tatusova TA An Adaptive Resolution Tree Visualization of Large Influenza Virus Sequence Datasets Bioinformatics Research and Applications, Proc. of ISBRA 2007, Volume LNBI 4463 of Lecture Notes in Bioinformatics Springer-Verlag Mandoiu I, Zelikovsky A 2007:192-202.
18. Levy PS Lemeshow S Sampling of Populations. Methods and Applications John Wiley and Sons 1999.
19. Weiss S Indurkhya N Zhang T Damerau F Text Mining: Predictive Methods for Analyzing Unstructured Information Springer-Verlag 2005.
20. Zaslavsky L Bao Y Tatusova TA Multiresolution approaches to representation and visualization of large influenza virus sequence datasets Data Mining in Bioinformatics Workshop (DMB 2007), Proc. of the IEEE International Conference on Bioinformatics and Biomedicine/ Workshops, November 2-4, 2007, IEEE 2007:109-114.
21. Plotkin JB Dushoff J Levin SA Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus PNAS 2002, 99(9):6263-6268. 122937 11972025 10.1073/pnas.082110799
22. Wolf YI Viboud C Holmes EC Koonin EV Lipman DJ Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus Biol Direct 2006, 1:34. 17067369 1647279 10.1186/ 1745-6150-1-34
23. Felsenstein J Inferring Phylogenies Cambridge University Press 2003
24. Bryant D A classification of consensus methods for phylogenies BioConsensus DIMACS, Americal Mathematical Society Janowitz M, Lapointe FJ, McMorris F, Mirkin B, Roberts F 2003:163-184.
25. Amenta N Clarke F St John K A Linear-Time Majority Tree Algorithm Algorithms in Bioinformatics, Proc. of WABI 2003, Volume LNBI 2812 of Lecture Notes in Bioinformatics Springer-Verlag Benson G, Page R 2003:216-227.