Interactive metagenomic visualization in a Web browser

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Ondov, Brian D ^a   Bergman, Nicholas H ^a   Phillippy, Adam M ^a  

^a National Biodefense Analysis and Countermeasures Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BROWSER-BASED APPLICATION; INTERACTIVE DISPLAY; INTUITIVE EXPLORATION; METAGENOMIC ANALYSIS; PREDICTION CONFIDENCE; RELATIVE ABUNDANCE; VISUALIZATION TOOLS; WEB-BASED ARCHITECTURE;

BIOINFORMATICS; FUNCTIONAL GROUPS; HTML; TOOLS; VISUALIZATION; WEB BROWSERS; WORLD WIDE WEB;

DATA VISUALIZATION;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; GASTROINTESTINAL TRACT; HUMAN; INTERNET; METAGENOMICS; METHODOLOGY; MICROBIOLOGY;

COMPUTATIONAL BIOLOGY; GASTROINTESTINAL TRACT; HUMANS; INTERNET; METAGENOMICS; SOFTWARE;

EID: 80053366291     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-385     Document Type: Article

References (23)

1. Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007, 17(3):377-386. 10.1101/gr.5969107, 1800929, 17255551.
2. Mitra S, Klar B, Huson DH. Visual and statistical comparison of metagenomes. Bioinformatics 2009, 25(15):1849-1855. 10.1093/bioinformatics/btp341, 19515961.
3. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9:386. 10.1186/1471-2105-9-386, 2563014, 18803844.
4. Goll J, Rusch D, Tanenbaum DM, Thiagarajan M, Li K, Methé BA, Yooseph S. METAREP: JCVI Metagenomics Reports - an open source tool for high-performance comparative metagenomics. Bioinformatics (Oxford, England) 2010,
5. Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS computational biology 2010, 6(2):e1000667. 10.1371/journal.pcbi.1000667, 2829047, 20195499.
6. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 2007, 73(16):5261-5267. 10.1128/AEM.00062-07, 1950982, 17586664.
7. Brady A, Salzberg S. PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nature methods 2011, 8(5):367. 10.1038/nmeth0511-367, 21527926.
8. Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nature methods 2009, 6(9):673-676. 10.1038/nmeth.1358, 2762791, 19648916.
9. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST: a better web interface. Nucleic Acids Research 2008, (36 Web Server):W5-9.
10. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
11. Andrews K, Heidegger H. Information slices: Visualising and exploring large hierarchies using cascading, semi-circular discs. Proc of IEEE Infovis' 98 1998,
12. Dix A, Beale R, Wood A. Architectures to make Simple Visualisations using Simple Systems. 2000,
13. Draper G, Livnat Y, Riesenfeld R. A Survey of Radial Methods for Information Visualization. Visualization and Computer Graphics, IEEE Transactions on 2009, 15(5):759-776.
14. Stasko J, Zhang E. Focus+Context Display and Navigation Techniques for Enhancing Radial, Space-Filling Hierarchy Visualizations. 2000,
15. Yang J, Ward M, Rundensteiner E. InterRing: an interactive tool for visually navigating and manipulating hierarchical structures. Information Visualization, 2002 INFOVIS 2002 IEEE Symposium on 2002, 77-84.
16. Johnson B, Shneiderman B. Tree-maps: a space-filling approach to the visualization of hierarchical information structures. Visualization, 1991 Visualization '91, Proceedings, IEEE Conference on 1991, 284-291.
17. Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology 2010, 11(8):R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864.
18. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 2011, (39 Database):D38-51.
19. Pham VD, Konstantinidis KT, Palden T, DeLong EF. Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environmental microbiology 2008, 10(9):2313-2330. 10.1111/j.1462-2920.2008.01657.x, 18494796.
20. Shneiderman B. The eyes have it: A task by data type taxonomy for information visualizations. Visual Languages 2002,
21. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428(6978):37-43. 10.1038/nature02340, 14961025.
22. Krona Homepage. , http://krona.sourceforge.net
23. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464(7285):59-65. 10.1038/nature08821, 20203603.