Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers

International Conference on Information and Knowledge Management, Proceedings

Volumn , Issue , 2009, Pages 3-10

  Yang, Bin ^a   Peng, Yu ^a   Leung, Henry C M ^a   Yiu, S M ^a   Chen, J C ^a   Chin, Francis Y L ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Binning; DNA composition features; k mean clustering; l mer; Metagenomics; Modified Chebychev distance

Indexed keywords

DATA SETS; DNA FRAGMENT; ERROR ROBUSTNESS; GENOME SEQUENCING; GENOMIC FRAGMENTS; GENOMICS; K-MEAN CLUSTERING; MARKER GENES; METAGENOMICS; MIXED SPECIES; RAPID DEVELOPMENT; RESEARCH METHODS; SEMI-SUPERVISED; SEQUENCING ERRORS; SOFTWARE TOOL; SOURCE CODES; SPECIES ABUNDANCE; SUB-STRINGS; TAXONOMIC CHARACTERIZATION; TRAINING DATA SETS;

BIOINFORMATICS; CLUSTERING ALGORITHMS; DNA; FORESTRY; KNOWLEDGE MANAGEMENT; MICROORGANISMS;

GENES;

EID: 74049111901     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1651318.1651322     Document Type: Conference Paper

References (25)

1. C. M. Cobb, "Microbes, inflammation, scaling and root planing, and the periodontal condition," J Dent Hyg, vol. 82 Suppl 3, pp. 4-9, Oct, 2008.
2. Z. A. Khachatryan, Z. A. Ktsoyan, G. P. Manukyan et al., "Predominant role of host genetics in controlling the composition of gut microbiota," PLoS One, vol. 3, no. 8, pp. e3064, 2008.
3. R. I. Amann, B. J. Binder, R. J. Olson et al., "Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations," Appl Environ Microbiol, vol. 56, no. 6, pp. 1919-25, Jun, 1990.
4. J. C. Venter, K. Remington, J. F. Heidelberg et al., "Environmental genome shotgun sequencing of the Sargasso Sea," Science, vol. 304, no. 5667, pp. 66-74, Apr 2, 2004.
5. G. W. Tyson, J. Chapman, P. Hugenholtz et al., "Community structure and metabolism through reconstruction of microbial genomes from the environment," Nature, vol. 428, no. 6978, pp. 37-43, Mar 4, 2004.
6. B. V. Jones, M. Begley, C. Hill et al., "Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome," Proc Natl Acad Sci U S A, vol. 105, no. 36, pp. 13580-5, Sep 9, 2008.
7. K. Mavromatis, N. Ivanova, K. Barry et al., "Use of simulated data sets to evaluate the fidelity of metagenomic processing methods," Nat Methods, vol. 4, no. 6, pp. 495-500, Jun, 2007.
8. S. F. Altschul, T. L. Madden, A. A. Schaffer et al., "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs," Nucleic Acids Res, vol. 25, no. 17, pp. 3389-402, Sep 1, 1997.
9. D. H. Huson, A. F. Auch, J. Qi et al., "MEGAN analysis of metagenomic data," Genome Res, vol. 17, no. 3, pp. 377-86, Mar, 2007.
10. J. R. Cole, B. Chai, R. J. Farris et al., "The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis," Nucleic Acids Res, vol. 33, no. Database issue, pp. D294-6, Jan 1, 2005.
11. H. Garcia Martin, N. Ivanova, V. Kunin et al., "Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities," Nat Biotechnol, vol. 24, no. 10, pp. 1263-9, Oct, 2006.
12. S. G. Tringe, C. von Mering, A. Kobayashi et al., "Comparative metagenomics of microbial communities," Science, vol. 308, no. 5721, pp. 554-7, Apr 22, 2005.
13. R. J. Case, Y. Boucher, I. Dahllof et al., "Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies," Appl Environ Microbiol, vol. 73, no. 1, pp. 278-88, Jan, 2007.
14. C. Desnues, B. Rodriguez-Brito, S. Rayhawk et al., "Biodiversity and biogeography of phages in modern stromatolites and thrombolites," Nature, vol. 452, no. 7185, pp. 340-3, Mar 20, 2008.
15. S. Karlin, and C. Burge, "Dinucleotide relative abundance extremes: a genomic signature," Trends Genet, vol. 11, no. 7, pp. 283-90, Jul, 1995.
16. S. Karlin, C. Burge, and A. M. Campbell, "Statistical analyses of counts and distributions of restriction sites in DNA sequences," Nucleic Acids Res, vol. 20, no. 6, pp. 1363-70, Mar 25, 1992.
17. S. Karlin, and I. Ladunga, "Comparisons of eukaryotic genomic sequences," Proc Natl Acad Sci U S A, vol. 91, no. 26, pp. 12832-6, Dec 20, 1994.
18. G. M. Rubin, M. D. Yandell, J. R. Wortman et al., "Comparative genomics of the eukaryotes," Science, vol. 287, no. 5461, pp. 2204-15, Mar 24, 2000.
19. R. Sandberg, G. Winberg, C. I. Branden et al., "Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier," Genome Res, vol. 11, no. 8, pp. 1404-9, Aug, 2001.
20. S. Karlin, J. Mrazek, and A. M. Campbell, "Compositional biases of bacterial genomes and evolutionary implications," J Bacteriol, vol. 179, no. 12, pp. 3899-913, Jun, 1997.
21. S. Chatterji, I. Yamazaki, Z. J. Bai et al., "CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads," Research in Computational Molecular Biology, Proceedings, vol. 4955, pp. 17-28, 480, 2008.
22. H. Teeling, A. Meyerdierks, M. Bauer et al., "Application of tetranucleotide frequencies for the assignment of genomic fragments," Environ Microbiol, vol. 6, no. 9, pp. 938-47, Sep, 2004.
23. H. Teeling, J. Waldmann, T. Lombardot et al., "TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences," BMC Bioinformatics, vol. 5, pp. 163, Oct 26, 2004.
24. A. C. McHardy, H. G. Martin, A. Tsirigos et al., "Accurate phylogenetic classification of variable-length DNA fragments," Nat Methods, vol. 4, no. 1, pp. 63-72, Jan, 2007.
25. N. N. Diaz, L. Krause, A. Goesmann et al., "TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach," BMC Bioinformatics, vol. 10, pp. 56, 2009.