title: Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers.
abstract: BACKGROUND
  With the rapid development of genome sequencing techniques, traditional research methods based on the isolation and cultivation of microorganisms are being gradually replaced by metagenomics, which is also known as environmental genomics. The first step, which is still a major bottleneck, of metagenomics is the taxonomic characterization of DNA fragments (reads) resulting from sequencing a sample of mixed species. This step is usually referred as "binning". Existing binning methods are based on supervised or semi-supervised approaches which rely heavily on reference genomes of known microorganisms and phylogenetic marker genes. Due to the limited availability of reference genomes and the bias and instability of marker genes, existing binning methods may not be applicable in many cases.
  
  
  RESULTS
  In this paper, we present an unsupervised binning method based on the distribution of a carefully selected set of l-mers (substrings of length l in DNA fragments). From our experiments, we show that our method can accurately bin DNA fragments with various lengths and relative species abundance ratios without using any reference and training datasets. Another feature of our method is its error robustness. The binning accuracy decreases by less than 1% when the sequencing error rate increases from 0% to 5%. Note that the typical sequencing error rate of existing commercial sequencing platforms is less than 2%.
  
  
  CONCLUSIONS
  We provide a new and effective tool to solve the metagenome binning problem without using any reference datasets or markers information of any known reference genomes (species). The source code of our software tool, the reference genomes of the species for generating the test datasets and the corresponding test datasets are available at http://i.cs.hku.hk/~alse/MetaCluster/.
authors.affiliation: State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096 PR China. byang@cs.hku.hk
authors.forename: Bin
authors.initials: B
authors.lastname: Yang
authors.forename: Yu
authors.initials: Y
authors.lastname: Peng
authors.forename: Henry Chi-Ming
authors.initials: HC
authors.lastname: Leung
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu
authors.forename: Jing-Chi
authors.initials: JC
authors.lastname: Chen
authors.forename: Francis Yuk-Lun
authors.initials: FY
authors.lastname: Chin
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D004247:DNA / Q000737:chemistry*; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D004783:Environmental Microbiology; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D007778:Lactobacillus / Q000235:genetics; D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA
references.citation: Science. 2004 Apr 2;304(5667):66-74
references.pmid: 15001713
references.citation: BMC Bioinformatics. 2004 Oct 26;5:163
references.pmid: 15507136
references.citation: Appl Environ Microbiol. 1990 Jun;56(6):1919-25
references.pmid: 2200342
references.citation: Nature. 2004 Mar 4;428(6978):37-43
references.pmid: 14961025
references.citation: Nature. 2008 Mar 20;452(7185):340-3
references.pmid: 18311127
references.citation: Science. 2000 Mar 24;287(5461):2204-15
references.pmid: 10731134
references.citation: Science. 2005 Apr 22;308(5721):554-7
references.pmid: 15845853
references.citation: Nucleic Acids Res. 1992 Mar 25;20(6):1363-70
references.pmid: 1313968
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D294-6
references.pmid: 15608200
references.citation: J Bacteriol. 1997 Jun;179(12):3899-913
references.pmid: 9190805
references.citation: PLoS One. 2008 Aug 26;3(8):e3064
references.pmid: 18725973
references.citation: Genome Res. 2001 Aug;11(8):1404-9
references.pmid: 11483581
references.citation: Nat Methods. 2007 Jun;4(6):495-500
references.pmid: 17468765
references.citation: Trends Genet. 1995 Jul;11(7):283-90
references.pmid: 7482779
references.citation: Environ Microbiol. 2004 Sep;6(9):938-47
references.pmid: 15305919
references.citation: BMC Bioinformatics. 2009 Feb 11;10:56
references.pmid: 19210774
references.citation: Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13580-5
references.pmid: 18757757
references.citation: Genome Res. 2007 Mar;17(3):377-86
references.pmid: 17255551
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Appl Environ Microbiol. 2007 Jan;73(1):278-88
references.pmid: 17071787
references.citation: Nat Biotechnol. 2006 Oct;24(10):1263-9
references.pmid: 16998472
references.citation: Nat Methods. 2007 Jan;4(1):63-72
references.pmid: 17179938
references.citation: Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12832-6
references.pmid: 7809130
references.citation: J Dent Hyg. 2008 Oct;82 Suppl 3:4-9
references.pmid: 19275822