Clustering metagenomic sequences with interpolated Markov models

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Kelley, David R ^a,b   Salzberg, Steven L ^a,b  

^a Bldg 142   (United States)

^b AV Williams Building ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING ACCURACY; COMPLEX DATASETS; EFFECTIVE APPROACHES; HIGHLY ACCURATE; MICROBIAL STRAIN; SEQUENCE CLUSTERING; SUPERVISED LEARNING METHODS; UNSUPERVISED APPROACHES;

BACTERIA; SUPERVISED LEARNING;

GENE ENCODING;

ARTICLE; AUTOMATED PATTERN RECOGNITION; CLUSTER ANALYSIS; DNA SEQUENCE; FACTUAL DATABASE; METAGENOMICS; METHODOLOGY; PROBABILITY;

CLUSTER ANALYSIS; DATABASES, FACTUAL; MARKOV CHAINS; METAGENOMICS; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ANALYSIS, DNA;

EID: 77958605377     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-544     Document Type: Article

References (54)

1. Liolios K, Chen I, Min A, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz V, Kyrpides N. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010, (38 Database):D346. 10.1093/nar/gkp848, 2808860, 19914934.
2. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'Haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009, 462(7276):1056-60. 10.1038/nature08656, 20033048.
3. Eisen JA. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol 2007, 5(3):e82. 10.1371/journal.pbio.0050082, 1821061, 17355177.
4. Rusch D, Halpern A, Sutton G, Heidelberg K, Williamson S, Yooseph S, Wu D, Eisen J, Hoffman J, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter J, Li K, Kravitz S, Heidelberg J, Utterback T, Rogers YH, Falcon L, Souza V, Bonilla-Rosso G, Eguiarte L, Karl D, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari M, Strausberg R, Nealson K, Friedman R, Frazier M, Venter C. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 2007, 5(3):e77. 10.1371/journal.pbio.0050077, 1821060, 17355176.
5. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial Community Variation in Human Body Habitats Across Space and Time. Science 2009, 326(5960):1694-1697. 10.1126/science.1177486, 19892944.
6. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Program NCS, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA. Topographical and Temporal Diversity of the Human Skin Microbiome. Science 2009, 324(5931):1190-1192. 10.1126/science.1171700, 2805064, 19478181.
7. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464(7285):59-65. 10.1038/nature08821, 20203603.
8. Hamady M, Knight R. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res 2009, 19(7):1141-1152. 10.1101/gr.085464.108, 19383763.
9. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428(6978):37-43. 10.1038/nature02340, 14961025.
10. Rodriguez-Brito B, Li L, Wegley L, Furlan M, Angly F, Breitbart M, Buchanan J, Desnues C, Dinsdale E, Edwards R, et al. Viral and microbial community dynamics in four aquatic environments. ISME J 2010,
11. Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor J, Nekrutenko A. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Res 2009, 19(11):2144. 10.1101/gr.094508.109, 2775585, 19819906.
12. Weinberg Z, Perreault J, Meyer M, Breaker R. Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature 2009, 462(7273):656-659. 10.1038/nature08586, 19956260.
13. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods 2007, 4(6):495-500. 10.1038/nmeth1043, 17468765.
14. Chen K, Pachter L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol 2005, 1(2):106-12. 10.1371/journal.pcbi.0010024, 1185649, 16110337.
15. McHardy A, Rigoutsos I. What's in the mix: phylogenetic classification of metagenome sequence samples. Curr Opin Microbiol 2007, 10(5):499-503. 10.1016/j.mib.2007.08.004, 17933580.
16. Navlakha S, White J, Nagarajan N, Pop M, Kingsford C. Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. Research in Computational Molecular Biology 2009, 400-417.
17. Wu M, Eisen J. A simple, fast, and accurate method of phylogenomic inference. Genome Biol 2008, 9(10):R151. 10.1186/gb-2008-9-10-r151, 2760878, 18851752.
18. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-402. 10.1093/nar/25.17.3389, 146917, 9254694.
19. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2010, (38 Database):D46-D51. 10.1093/nar/gkp1024, 2808980, 19910366.
20. Gerlach W, Junemann S, Tille F, Goesmann A, Stoye J. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics 2009, 10:430. 10.1186/1471-2105-10-430, 2801688, 20021646.
21. Haque MM, Ghosh T, Komanduri D, Mande S. SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics 2009, 25(14):1722-1730. 10.1093/bioinformatics/btp317, 19439565.
22. Huson D, Auch A, Qi J, Schuster S. MEGAN analysis of metagenomic data. Genome Res 2007, 17(3):377-386. 10.1101/gr.5969107, 1800929, 17255551.
23. Koski LB, Golding GB. The closest BLAST hit is often not the nearest neighbor. J Mol Evol 2001, 52(6):540-2.
24. Karlin S, Mrazek J, Campbell AM. Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 1997, 179(12):3899-913. 179198, 9190805.
25. Bohlin J, Skjerve E, Ussery D. Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering. BMC Genomics 2009, 10:487. 10.1186/1471-2164-10-487, 2770534, 19845945.
26. Mann S, Chen YP. Bacterial genomic G+C composition-eliciting environmental adaptation. Genomics 2010, 95:7-15. 10.1016/j.ygeno.2009.09.002, 19747541.
27. Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T. Informatics for unveiling hidden genome signatures. Genome Res 2003, 13(4):693-702. 10.1101/gr.634603, 430167, 12671005.
28. Teeling H, Meyerdierks A, Bauer M, Amann R, Glockner F. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 2004, 6(9):938-947. 10.1111/j.1462-2920.2004.00624.x, 15305919.
29. Bohlin J, Skjerve E, Ussery D. Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes. PLoS Comput Biol 2008, 4(4):e1000057. 10.1371/journal.pcbi.1000057, 2289840, 18421372.
30. Mrazek J. Phylogenetic Signals in DNA Composition: Limitations and Prospects. Mol Biol Evol 2009, 26(5):1163-1169. 10.1093/molbev/msp032, 19233962.
31. Lee SJ, Mortimer JR, Forsdyke DR. Genomic conflict settled in favour of the species rather than the gene at extreme GC percentage values. Appl Bioinformatics 2004, 3(4):219-28. 10.2165/00822942-200403040-00003, 15702952.
32. Lawrence JG, Ochman H. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997, 44(4):383-97. 10.1007/PL00006158, 9089078.
33. Dick G, Andersson A, Baker B, Simmons S, Thomas B, Yelton P, Banfield J. Community-wide analysis of microbial genome sequence signatures. Genome Biol 2009, 10(8):R85. 10.1186/gb-2009-10-8-r85, 2745766, 19698104.
34. 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 2009, 10:56. 10.1186/1471-2105-10-56, 2653487, 19210774.
35. McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 2007, 4:63-72. 10.1038/nmeth976, 17179938.
36. Abe T, Sugawara H, Kinouchi M, Kanaya S, Ikemura T. Novel Phylogenetic Studies of Genomic Sequence Fragments Derived from Uncultured Microbe Mixtures in Environmental and Clinical Samples. DNA Res 2005, 12(5):281. 10.1093/dnares/dsi015, 16769690.
37. Sandberg R, Winberg G, Branden CI, Kaske A, Ernberg I, Coster J. Capturing Whole-Genome Characteristics in Short Sequences Using a Naive Bayesian Classifier. Genome Res 2001, 11(8):1404-1409. 10.1101/gr.186401, 311094, 11483581.
38. Brady A, Salzberg S. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 2009, 6(9):673-676. 10.1038/nmeth.1358, 2762791, 19648916.
39. Chatterji S, Yamazaki I, Bai Z, Eisen J. CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads. Research in Computational Molecular Biology 2008, 17-28.
40. Kislyuk A, Bhatnagar S, Dushoff J, Weitz J. Unsupervised statistical clustering of environmental shotgun sequences. BMC Bioinformatics 2009, 10:316. 10.1186/1471-2105-10-316, 2765972, 19799776.
41. Chan CKK, Hsu A, Tang SL, Halgamuge S. Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing. J Biomed Biotechnol 2008, 2008.
42. Wu YW, Ye Y. A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples. Research in Computational Molecular Biology, of Lecture Notes in Computer Science 2010, 6044:535-549. Springer Berlin/Heidelberg, Berger B.
43. Bohlin J, Skjerve E, Ussery D. Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes. BMC Genomics 2008, 9:104. 10.1186/1471-2164-9-104, 2289816, 18307761.
44. Smyth P. Clustering Sequences with Hidden Markov Models. Advances in Neural Information Processing Systems 1997, 9:648-654.
45. Durbin R, Eddy S, Krogh A, Mitchison G. Biological sequence analysis 1998, Cambridge University Press.
46. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27(23):4636-4641. 10.1093/nar/27.23.4636, 148753, 10556321.
47. Salzberg SL, Delcher AL, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998, 26(2):544-548. 10.1093/nar/26.2.544, 147303, 9421513.
48. Celeux G, Govaert G. A classification EM algorithm for clustering and two stochastic versions. Computational Statistics and Data Analysis 1992, 14(3):315-332.
49. Shi J, Malik J. Normalized cuts and image segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence 2000, 22(8):888-905.
50. Tan P, Steinbach M, Kumar V. Introduction to Data Mining 2006, Addison-Wesley.
51. Hubert L, Arabie P. Comparing partitions. Journal of Classification 1985, 2:193-218.
52. Morgan J, Darling A, Eisen J. Metagenomic sequencing of an in vitro-simulated microbial community. PloS ONE 2010, 5(4):e10209. 10.1371/journal.pone.0010209, 2855710, 20419134.
53. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23(6):673. 10.1093/bioinformatics/btm009, 2387122, 17237039.
54. White J, Navlakha S, Nagarajan N, Ghodsi M, Kingsford C, Pop M. Alignment and clustering of phylogenetic markers- implications for microbial diversity studies. BMC Bioinformatics 2010, 11:152. 10.1186/1471-2105-11-152, 2859756, 20334679.