Genomic signatures for metagenomic data analysis: Exploiting the reverse complementarity of tetranucleotides

2011 IEEE International Conference on Systems Biology, ISB 2011

Volumn , Issue , 2011, Pages 149-154

  Gori, Fabio ^a   Mavroedis, Dimitrios ^a   Jetten, Mike S M ^a   Marchiori, Elena ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

Author keywords

genome signature; metagenome binning; metagenomic data analysis; metagenomics; taxonomic annotation

Indexed keywords

DATA SETS; DIRECT USE; GENERAL PURPOSE; GENOMIC FRAGMENTS; IN-SILICO; MACHINE LEARNING METHODS; METAGENOMES; METAGENOMIC DATA ANALYSIS; METAGENOMICS; MICROBIAL COMMUNITIES; ONLINE SUPPLEMENTARY MATERIAL; TAXONOMIC ANNOTATION;

DATA REDUCTION; EXPERIMENTS; LEARNING SYSTEMS; OLIGONUCLEOTIDES; RNA;

GENES;

EID: 80054864492     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ISB.2011.6033147     Document Type: Conference Paper

References (29)

1. S. Karlin and C. Burge, "Dinucleotide relative abundance extremes: a genomic signature." Trends in Genetics, vol. 11, no. 7, pp. 283-290, Jul. 1995.
2. S. Karlin et al., "Comparative DNA analysis across diverse genomes", Annual review of genetics, vol. 32, no. 1, pp. 185-225, 1998.
3. J. Bohlin, "Genomic signatures in microbes - properties and applications", The Scientific World Journal, vol. 11, pp. 715-725, 2011.
4. M. W. van Passel et al., "The reach of the genome signature in prokaryotes." BMC Evolutionary Biology, vol. 6, pp. 84+, Oct. 2006.
5. J. Bohlin et al., "Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering", BMC Genomics, vol. 10, no. 1, pp. 487+, 2009.
6. J. Mrázek, "Phylogenetic signals in DNA composition: Limitations and prospects", Molecular Biology and Evolution, vol. 26, no. 5, pp. 1163-1169, 2009.
7. J. C. Wooley, A. Godzik, and I. Friedberg, "A primer on metagenomics." PLoS Comput Biol, vol. 6, no. 2, p. e1000667, Feb. 2010.
8. Y.-W. W. Wu et al., "A novel abundance-based algorithm for binning metagenomic sequences using l-tuples", Journal of computational biology: a journal of computational molecular cell biology, vol. 18, no. 3, pp. 523-534, Mar. 2011.
9. A. Brady et al., "Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models", Nature Methods, vol. 6, no. 9, pp. 673-676, August 2009.
10. D. Kelley et al., "Clustering metagenomic sequences with interpolated Markov models", BMC Bioinformatics, vol. 11, no. 1, pp. 544+, Nov. 2010.
11. D. H. Huson et al., "Megan analysis of metagenomic data", Genome Research, vol. 17, no. 3, pp. 377-386, March 2007.
12. L. Krause et al., "Phylogenetic classification of short environmental DNA fragments", Nucleic Acids Research, vol. 36, no. 7, pp. 2230-2239, 2008.
13. H. Teeling et al., "Application of tetranucleotide frequencies for the assignment of genomic fragments", Environmental Microbiology, vol. 6, no. 9, pp. 938-947, 2004.
14. C.-K. K. K. Chan et al., "Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing", Journal of Biomedicine and Biotechnology, vol. 2008, no. 1, 2008.
15. S. Chatterji et al., "CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads", in RECOMB 2008, ser. LNCS, 2008, vol. 4955, ch. 3, pp. 17-28.
16. A. Kislyuk et al., "Unsupervised statistical clustering of environmental shotgun sequences", BMC Bioinformatics, vol. 10, no. 1, pp. 316+, 2009.
17. M. H. Mohammed et al., "SPHINX-an algorithm for taxonomic binning of metagenomic sequences." Bioinformatics, vol. 27, no. 1, pp. 22-30, Jan 2011.
18. B. Yang et al., "Metacluster: unsupervised binning of environmental genomic fragments and taxonomic annotation", in BCB. ACM, 2010, pp. 170-179.
19. K. R. Patil et al., "Taxonomic metagenome sequence assignment with structured output models", Nature Methods, vol. 8, no. 3, pp. 191-192, Mar. 2011.
20. N. N. Diaz et al., "TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach", BMC Bioinformatics, vol. 10, no. 1, pp. 56+, 2009.
21. O. Nalbantoglu et al., "RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles", BMC Bioinformatics, vol. 12, no. 1, pp. 41+, 2011.
22. I. Saeed et al., "The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments." BMC Genomics, vol. 10 Suppl 3, p. S10, 2009.
23. D. T. Pride et al., "Evolutionary implications of microbial genome tetranucleotide frequency biases", Genome Research, vol. 13, no. 2, pp. 145-158, 2003.
24. J. Lin, "Divergence measures based on the Shannon entropy", IEEE Transactions on Information Theory, vol. 37, no. 1, pp. 145-151, Jan. 1991.
25. E. W. Sayers et al., "Database resources of the National Center for Biotechnology Information", Nucleic Acids Research, vol. 37, no. suppl 1, pp. D5-D15, 2009.
26. T. Fawcett, "An introduction to ROC analysis", Pattern Recognition Letters, vol. 27, no. 8, pp. 861-874, Jun. 2006.
27. M. Hollander and D. A. Wolfe, Nonparametric Statistical Methods, 2nd Edition, 2nd ed. Wiley-Interscience, Jan. 1999.
28. E. Jones, T. Oliphant, P. Peterson et al., "SciPy: Open source scientific tools for Python", 2001-. [Online]. Available: http://www.scipy.org/
29. S. C. Perry and R. G. Beiko, "Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives." Genome biology and evolution, vol. 2, no. 0, pp. 117-131, Jan. 2010.