A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio

Bioinformatics

Volumn 27, Issue 11, 2011, Pages 1489-1495

  Leung, Henry C M ^a   Yiu, S M ^a   Yang, Bin ^a   Peng, Yu ^a   Wang, Yi ^a   Liu, Zhihua ^a   Chen, Jingchi ^a   Qin, Junjie ^a   Li, Ruiqiang ^b   Chin, Francis Y L ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b BGI SHENZHEN   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; DNA SEQUENCE; METAGENOMICS; METHODOLOGY;

ALGORITHMS; CLUSTER ANALYSIS; METAGENOMICS; SEQUENCE ANALYSIS, DNA;

EID: 79957877228     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr186     Document Type: Article

References (28)

1. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Amann,R.I. et al. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol., 56, 1919-1925.
3. Case,R.J. et al. (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl. Environ. Microbiol., 73, 278-288.
4. Chan,C.K. et al. (2008) Binning sequences using very sparse labels within a metagenome. BMC Bioinformatics, 9, 215.
5. Chatterji,S. et al. (2008) A DNA composition-based algorithm for binning environmental shotgun reads. Res. Comp. Mole. Biol., 17-28.
6. Chor,B. et al. (2009) Genomic DNA k-mer spectra: models and modalities. Genome Biol., 10, R108.
7. Cole,J.R. et al. (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res., 33, D294-D296.
8. Diaconis,P. and Graham, R.L. (1977) Spearman's Footrule as a measure of disarray. J. R. Stat. Soc. Ser. B, 39, 262-268.
9. Garcia Martin, H. et al. (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol., 24, 1263-1269.
10. Huson,D.H. et al. (2007) MEGAN analysis of metagenomic data. Genome Res., 17, 377-386.
11. Jain,A.K. and Dubes,R.C. (1981) Algorithms for Clustering Data. Prentice-Hall, Upper Saddle River, NJ, USA.
12. Jones,B.V. et al. (2008) Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc. Natl Acad. Sci. USA, 105, 13580-13585.
13. Karlin,S. and Burge,C. (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends Genet., 11, 283-290.
14. Karlin,S. and Ladunga,I. (1994) Comparisons of eukaryotic genomic sequences. Proc. Natl Acad. Sci. USA, 91, 12832-12836.
15. Karlin,S., et al. (1997) Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol., 179, 3899-3913.
16. Kendall,M.G. (1938) A new measure of rank correlation. Biometrika, 30, 81-93.
17. Khachatryan,Z.A. et al. (2008) Predominant role of host genetics in controlling the composition of gut microbiota. PLoS One, 3, e3064.
18. Kislyuk, A. et al. (2009) Unsupervised statistical clustering of environmental shotgun sequences. BMC Bioinformatics, 10, 316.
19. Mavromatis,K. et al. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat. Methods, 4, 495-500.
20. Qin,J. et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59-65.
21. Teeling,H. et al. (2004) TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics, 5, 163.
22. Tringe,S.G. et al. (2005) Comparative metagenomics of microbial communities. Science, 308, 554-557.
23. Tyson,G.W. et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428, 37-43.
24. Venter,J.C. et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304, 66-74.
25. Wu,Y.W. and Ye, Y. (2010) A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. Res. Comp. Mole. Biol., 535-549.
26. Yang,B. et al. (2009) Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. In Data and Text Mining in Biomedical Informatics '09, pp. 3-10.
27. Yang,B. et al. (2010) MetaCluster: unsupervised binning of environmental genomic fragments and taxonomic annotation. In ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), pp. 170-179.
28. Zhou,F. et al. (2008) Barcodes for genomes and applications. BMC Bioinformatics, 9, 546.