Accurate taxonomic assignment of short pyrosequencing reads

Pacific Symposium on Biocomputing 2010, PSB 2010

Volumn , Issue , 2010, Pages 3-9

  Clemente, José C ^a   Jansson, Jesper ^b   Valiente, Gabriel ^c  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b OCHANOMIZU UNIVERSITY   (Japan)

^c UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DATA SETS; LOWEST COMMON ANCESTORS; MICROBIOTAS; PRECISION AND RECALL; PYROSEQUENCING; SUBTREES; SUFFIX ARRAYS;

MAPPING;

TAXONOMIES;

BACTERIAL RNA; RNA 16S;

ANIMAL; ARTICLE; BACTERIUM; BIOLOGY; CLASSIFICATION; DIGESTIVE SYSTEM; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METAGENOME; METAGENOMICS; METHODOLOGY; MICROBIOLOGY; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICS;

ANIMALS; BACTERIA; COMPUTATIONAL BIOLOGY; DIGESTIVE SYSTEM; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOME; METAGENOMICS; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 77954314824     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (41)

1. J. Shendure and H. Ji, Nature Biotechnology 26, 1135 (2008).
2. P. J. Turnbaugh, R. E. Ley, M. Hamady, C. M. Fraser-Liggett, R. Knight and J. I. Gordon, Nature 449, 804 (2007).
3. J. Venter, K. Remington, J. Heidelberg, A. Halpern, D. Rusch, J. Eisen, D. Wu, I. Paulsen, K. Nelson, W. Nelson, D. Fouts, S. Levy, A. Knap, M. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden- Tillson, C. Pfannkoch, Y. Rogers and H. Smith, Science 304, 66 (2004).
4. P. D. Schloss and J. Handelsman, Applied and Environmental Microbiology 71, 1501 (2005).
5. P. D. Schloss and J. Handelsman, Applied and Environmental Microbiology 72, 6773 (2006).
6. P. D. Schloss and J. Handelsman, BMC Bioinformatics 9, p. 34 (2008).
7. V. Seguritan and F. Rohwer, BMC Bioinformatics 2, p. 9 (2001).
8. C. Lozupone and R. Knight, Applied and Environmental Microbiology 71, 8228 (2005).
9. A. Martin, Applied and Environmental Microbiology 68, 3673 (2002).
10. P. D. Schloss and J. Handelsman, Applied and Environmental Microbiology 72, 2379 (2005).
11. D. Singleton, M. Furlong, S. Rathbun and W. Whitman, Applied and Environmental Microbiology 67, 4374 (2001).
12. T. Abe, H. Sugawara, M. Kinouchi, S. Kanaya and T. Ikemura, DNA Research 12, 281 (2005).
13. C. Martin, N. N. Diaz, J. Ontrup and T. W. Nattkemper, Bioinformatics 24, 1568 (2008).
14. A. C. McHardy, H. G. Martiń, A. Tsirigos, P. Hugenholtz and I. Rigoutsos, Nature Methods 4, 63 (2007).
15. H. Teeling, A. Meyerdierks, M. Bauer, R. Amann and F. O. Glöckner, Environmental Microbiology 6, 938 (2004).
16. N. N. Diaz, L. Krause, A. Goesmann, K. Niehaus and T. W. Nattkemper, BMC Bioinformatics 10, p. 56 (2009).
17. J. R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity and J. M. Tiedje, Nucleic Acids Research 37, 141 (2009).
18. D. H. Huson, A. F. Auch, J. Qi and S. C. Schuster, Genome Research 17, 377 (2007).
19. Z. Liu, T. Z. DeSantis, G. L. Andersen and R. Knight, Nucleic Acids Research 36, p. e120 (2008).
20. Q. Wang, G. M. Garrity, J. M. Tiedje and J. R. Cole, Applied and Environmental Microbiology 73, 5261 (2007).
21. L. Krause, N. N. Diaz, A. Goesmann, S. Kelley, T. W. Nattkemper, F. Rohwer, R. A. Edwards and J. Stoye, Nucleic Acids Research 36, 2230 (2008).
22. B. Langmead, C. Trapnell, M. Pop and S. L. Salzberg, Genome Biology 10, p. R25 (2009).
23. H. Li and R. Durbin, Bioinformatics 25, 1754 (2009).
24. R. Li, Y. Li, K. Kristiansen and J. Wang, Bioinformatics 24, 713 (2008).
25. N. Malhis, Y. Butterfield, M. Ester and S. J. M. Jones, Bioinformatics 25, 6 (2009).
26. H. G. Martiń, N. Ivanova, V. Kunin, F. Warnecke, K. W. Barry, A. C. McHardy, C. Yeates, S. He, A. A. Salamov, E. Szeto, E. Dalin, N. H. Putnam, H. J. Shapiro, J. L. Pangilinan, I. Rigoutsos, N. C. Kyrpides, L. L. Blackall, K. D. McMahon and P. Hugenholtz, Nature Biotechnology 24, 1263 (2006).
27. G. Valiente, Algorithms on Trees and Graphs (Springer, 2002).
28. G. Valiente, Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R (Taylor & Francis/CRC Press, 2009).
29. M. A. Bender, M. Farach-Colton, G. Pemmasani, S. Skiena and P. Sumazin, Journal of Algorithms 57, 75 (2005).
30. M. L. Sogin, H. G. Morrison, J. A. Huber, D. M. Welch, S. M. Huse, P. R. Neal, J. M. Arrieta and G. J. Herndl, Proc. Natl. Acad. Sci. USA 103, 12115 (2006).
31. P. J. Turnbaugh, M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan, R. E. Ley, M. L. Sogin, W. J. Jones, B. A. Roe, J. P. Affourtit, M. Egholm, B. Henrissat, A. C. Heath, R. Knight and J. I. Gordon, Nature 457, 480 (2009).
32. R. E. Ley, C. Lozupone, M. Hamady, R. Knight and J. I. Gordon, Nature Reviews Microbiology 6, 776 (2008).
33. E. A. Dinsdale, R. A. Edwards, D. Hall, F. Angly, M. Breitbart, J. M. Brulc, M. Furlan, C. Desnues, M. Haynes, L. Li, L. McDaniel, M. A. Moran, K. E. Nelson, C. Nilsson, R. Olson, J. Paul, B. R. Brito, Y. Ruan, B. K. Swan, R. Stevens, D. L. Valentine, R. V. Thurber, L. Wegley, B. A. White and F. Rohwe, Nature 452, 629 (2008).
34. Z. Liu, C. Lozupone, M. Hamady, F. D. Bushman and R. Knight, Nucleic Acids Research 35, p. e120 (2007).
35. C. Manichanh, C. E. Chapple, L. Frangeul, K. Gloux, R. Guigó and J. Dore, Nucleic Acids Research 36, 5180 (2008).
36. L. Dethlefsen, S. Huse, M. L. Sogin and D. A. Relman, PLoS Biology 6, p. e280 (2008).
37. VAMPS, Visualization and analysis of microbial population structure project, AGT CKN Bv6-Chicken intestinal microbiota, (2009).
38. C. Manichanh, Rat intestinal microbiota, Private communication, (2009).
39. P. Ribeca, GEM-GEnomic Multi-tool, http://gemlibrary.sourceforge.net/, (2009).
40. L. Dethlefsen, M. McFall-Ngai and D. A. Relman, Nature 449, 811 (2007).
41. R. E. Ley, D. Peterson and J. I. Gordon, Cell 124, 837 (2006).