MetaPhyler: Taxonomic profiling for metagenomic sequences

Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010

Volumn , Issue , 2010, Pages 95-100

  Liu, Bo ^a,b   Gibbons, Theodore ^a,c   Ghodsi, Mohammad ^a,b   Pop, Mihai ^a,b  

^a Bldg 142   (United States)

^b University of Maryland ^*  (United States)

^c UNIVERSITY OF MARYLAND   (United States)

Author keywords

Metagenomics; Phylogenetic classification; Taxonomic profiling

Indexed keywords

16S RRNA; 16S RRNA GENE; CLASSIFICATION RESULTS; COPY NUMBER; DATA SETS; INDIVIDUAL SEQUENCES; MARKER GENES; METAGENOMES; METAGENOMICS; MICROBIAL DIVERSITY; PHYLOGENETIC CLASSIFICATIONS; SIMULATED DATASETS; TAXONOMIC COMPOSITION; TAXONOMIC PROFILING;

BIOINFORMATICS; RNA;

GENES;

EID: 79952426696     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2010.5706544     Document Type: Conference Paper

References (19)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J.: Basic local alignment search tool, J Mol Biol, 1990, 215, (3), pp. 403-410
2. Brady, A., and Salzberg, S.L.: Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models, Nat Methods, 2009, 6, (9), pp. 673-676
3. Gerlach, W., Junemann, S., Tille, F., Goesmann, A., and Stoye, J.: WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads, BMC Bioinformatics, 2009, 10, pp. 430
4. Hamady, M., and Knight, R.: Microbial community profiling for human microbiome projects: Tools, techniques, and challenges, Genome Res, 2009, 19, (7), pp. 1141-1152
5. Handelsman, J.: Metagenomics: application of genomics to uncultured microorganisms, Microbiol Mol Biol Rev, 2004, 68, (4), pp. 669-685
6. Hooper, L.V., and Gordon, J.I.: Commensal host-bacterial relationships in the gut, Science, 2001, 292, (5519), pp. 1115-1118
7. Huson, D.H., Auch, A.F., Qi, J., and Schuster, S.C.: MEGAN analysis of metagenomic data, Genome Res, 2007
8. Krause, L., Diaz, N.N., Goesmann, A., Kelley, S., Nattkemper, T.W., Rohwer, F., Edwards, R.A., and Stoye, J.: Phylogenetic classification of short environmental DNA fragments, Nucleic acids research, 2008, 36, (7), pp. 2230-2239
9. McHardy, A.C., Martin, H.G., Tsirigos, A., Hugenholtz, P., and Rigoutsos, I.: Accurate phylogenetic classification of variable-length DNA fragments, Nat Methods, 2007, 4, (1), pp. 63-72
10. Parks, D.H., and Beiko, R.G.: Identifying biologically relevant differences between metagenomic communities, Bioinformatics (Oxford, England), 2010, 26, (6), pp. 715-721
11. Riesenfeld, C.S., Schloss, P.D., and Handelsman, J.: Metagenomics: genomic analysis of microbial communities, Annual review of genetics, 2004, 38, pp. 525-552
12. Sommer, D.D., Delcher, A.L., Salzberg, S.L., and Pop, M.: Minimus: a fast, lightweight genome assembler, BMC bioinformatics, 2007, 8, pp. 64
13. Tringe, S.G., and Hugenholtz, P.: A renaissance for the pioneering 16S rRNA gene, Current opinion in microbiology, 2008, 11, (5), pp. 442-446
14. Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P., Egholm, M., Henrissat, B., Heath, A.C., Knight, R., and Gordon, J.I.: A core gut microbiome in obese and lean twins, Nature, 2009, 457, (7228), pp. 480-484
15. von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., Ward, N., and Bork, P.: Quantitative phylogenetic assessment of microbial communities in diverse environments, Science, 2007, 315, (5815), pp. 1126-1130
16. Wang, Q., Garrity, G.M., Tiedje, J.M., and Cole, J.R.: Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl Environ Microbiol, 2007, 73, (16), pp. 5261-5267
17. White, J.R., Nagarajan, N., and Pop, M.: Statistical methods for detecting differentially abundant features in clinical metagenomic samples, PLoS computational biology, 2009, 5, (4), pp. e1000352
18. Wu, M., and Eisen, J.A.: A simple, fast, and accurate method of phylogenomic inference, Genome Biol, 2008, 9, (10), pp. R151
19. Zhang, H., DiBaise, J.K., Zuccolo, A., Kudrna, D., Braidotti, M., Yu, Y., Parameswaran, P., Crowell, M.D., Wing, R., Rittmann, B.E., and Krajmalnik-Brown, R.: Human gut microbiota in obesity and after gastric bypass, Proc Natl Acad Sci U S A, 2009, 106, (7), pp. 2365-2370