Short prokaryotic DNA fragment binning using a hierarchical classifier based on linear discriminant analysis and principal component analysis

Journal of Bioinformatics and Computational Biology

Volumn 8, Issue 6, 2010, Pages 995-1011

  Zheng, Hao ^a   Wu, Hongwei ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Binning; linear discriminant analysis; metagenomics; principal component analysis

Indexed keywords

PROKARYOTA; TETRA;

DNA;

ALGORITHM; ARTICLE; BIOLOGY; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER SIMULATION; DISCRIMINANT ANALYSIS; DNA SEQUENCE; EVALUATION; GENE LIBRARY; GENETICS; HORIZONTAL GENE TRANSFER; METAGENOME; METAGENOMICS; MICROBIAL GENETICS; NUCLEIC ACID DATABASE; PRINCIPAL COMPONENT ANALYSIS; STATISTICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, NUCLEIC ACID; DISCRIMINANT ANALYSIS; DNA; GENE LIBRARY; GENE TRANSFER, HORIZONTAL; GENETICS, MICROBIAL; METAGENOME; METAGENOMICS; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 78649820297     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720010005051     Document Type: Article

References (38)

1. Chen K, Pachter K, Bioinformatics for whole-genome shotgun sequencing of microbial communities, PLoS Comput Biol 1(2):106-112, 2005.
2. Lorenz P, Eck J, Metagenomics and industrial applications, Nat Rev Microbiol 3(6):510-516, 2005.
3. Uchiyama T, Abe T, Ikemura T, Watanabe K, Substrateinduced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes, Nat Biotechnol 23(1):88-93, 2005.
4. Beja O, Aravind L, Koonin E, Suzuki M, Hadd A, Nguyen L, Jovanovich S, Gates C, Feldman R, Spudich J, Spudich E, DeLong E, Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea, Science 289(5486):1902-1906, 2000.
5. Liles M, Manske B, Bintrim S, Handelsman J, Goodman R, A census of rrna genes and linked genomic sequences within a soil metagenomic library, Appl Environ Microbiol 69(5):2684-2691, 2003.
6. Venter J, Remington K, Heidelberg J, Halpern A, Rusch D, Eisen J, Wu D, Paulsen I, Nelson K, Nelson W, Fouts D, Levy S, Knap A, Lomas M, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Tillson H, Pfannkoch C, Rogers Y, Smith H, Environmental genome shotgun sequencing of the sargasso sea, Science 304:66-74, 2004.
7. Wu H, PCA-based linear combinations of k-mer frequencies for metagenomic DNA fragment binning, in IEEE CIBCB, pp. 46-53, 2008.
8. Tyson G, Chapman J, Hugenholtz P, Allen E, Ram R, Richardson P, Solovyev V, Rubin E, Rokhsar D, Banfield J, Community structure and metabolism through reconstruction of microbial genomes from the environment, Nature 428:37-43, 2004.
9. Eisen J, Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes, PLoS Biol 5(3):e82, 2007.
10. Batzoglou S, Algorithmic challenges in mammalian genome sequence assembly, in Dunn M, Jorde L, Little P, Subramaniam S (eds.), Encyclopedia of Genomics, Proteomics and Bioinformatics, 2005.
11. Chan C, Hsu A, Tang S, Halgamuge S, Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing, J Biomed Biotechnol 2008:513701, 2008.
12. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy A, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides N, Use of simulated data sets to evaluate the fidelity of metagenomic processing methods, Nature Methods 4(6):495-500, 2007.
13. Huson H, Auch A, Qi J, Schuster S, Megan analysis of metagenomic data, Genome Res 17:377-386, 2007.
14. Krause L, Diaz N, Goesmann A, Kelley S, Nattkemper T, Rohwer F, Edwards R, Stoye J, Phylogenetic classification of short environmental DNA fragments, Nucleic Acids Res, pp. 1-10, 2008.
15. Arima K, Wooley J, Computational Methods for Understanding Archaeal and Bacterial Genomes. Imperial College Press, 2008, ch. Metagenomics.
16. Abe T, Sugawara H, Kanaya S, Ikemura T, A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental microbes, Polar Biosci 20:103-112, 2006.
17. Chan K, Hsu A, Halgamuge S, Tang S, Binning sequences using very sparse labels within a metagenome, BMC Bioinformatics 9(1):215, 2008.
18. Teeling H, Waldmann J, Lombardot T, Bauer M, Glockner F, 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, 2004.
19. McHardy A, Martin H, Tsirigos A, Hugenholtz P, Rigoutsos I, Accurate phylogenetic classification of variable-length DNA fragments, Nature Methods 4(1):63-72, 2007.
20. Chatterji S, Yamazaki I, Bai Z, Eisen JA, Compostbin: A DNA composition-based algorithm for binning environmental shotgun reads, Lect Notes Comput Sci 4955:17, 2008.
21. Brady A, Salzberg S, Phymm and phymmbl: Metagenomic phylogenetic classification with interpolated markov models, Nature Methods 6:673-676, 2009.
22. Diaz N, Krause L, Goesmann A, Niehaus K, Nattkemper T, TACOA-taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach, BMC Bioinformatics 10:56, 2009.
23. Zheng H, Wu H, A novel LDA and PCA-based hierarchical scheme for metagenomic fragment binning, in IEEE CIBCB, pp. 53-59, 2009.
24. Bohlin J, Skjerve E, Ussery DW, Investigations of oligonucleotide usage variance within and between prokaryotes, PLoS Comput. Biol 4(4):e1000057, 2008.
25. Forbes K, Fiume E, An efficient search algorithm for motion data using weighted pca, Proceedings of the 2005 ACM SIGGRAPH/Eurographics Symposium on Computer Animation, pp. 67-76, 2005.
26. http://www.cis.hut.fi/~jhollmen/dippa/node30.html.
27. Wall ME, Rechtsteiner A, Rocha LM, Singular value decomposition and principal component analysis, A Practical Approach to Microarray Data Analysis. Norwell, MA: Kluwer, 2003, pp. 91-109.
28. Duda R, Hart P, Stork D, Pattern Classification, 2nd ed., John Wiley & Sons, 2001.
29. Ng A, Jordan M, On discriminative vs. generative classifiers: A comparison of logistic regression and naive bayes, NIPS, 14: 2002.
30. http://fames.jgi-psf.orgcgi-bindataset-desc.pl?dataset=all
31. http://www.genome.jp/kegg/
32. http://cbcsrv.watson.ibm.com/phylopythia.html
33. Teeling H, Meyerdierks A, Bauer M, Amann R, Glockner F, Application of tetranu-cleotide frequencies for the assignment of genomic fragments, Environ Microbiol 6:938-947, 2004.
34. Wellner A, Gophna U, Complexity, connectivity, and duplicability as barriers to lateral gene transfer, Genome Biology 8(8):R156, 2007.
35. Podell S, Gaasterland1 T, Allen E, A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the darkhorse algorithm, BMC Bioinformatics 9:419, 2008.
36. Koonin EV, Makarova KS, Aravind L, Horizontal gene transfer in prokaryotes: Quantification and classification, Annu Rev Microbiol 55:709C42, 2001.
37. Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV, Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles, Trends Genet 14: 442-444, 1998.
38. Mrazek J, Gaynon L, Karlin S, Frequent oligonucleotide motifs in genomes of three streptococci, Nucleic Acids Res 30(19):4216-4221, 2002.