TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW (2009)
BMC Bioinformatics 10(1): 56.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Background: Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning. Results Our novel strategy was extensively evaluated using the leave-one-out cross validation strategy on fragments of variable length (800 bp – 50 Kbp) from 373 completely sequenced genomes. TACOA is able to classify genomic fragments of length 800 bp and 1 Kbp with high accuracy until rank class. For longer fragments ≥ 3 Kbp accurate predictions are made at even deeper taxonomic ranks (order and genus). Remarkably, TACOA also produces reliable results when the taxonomic origin of a fragment is not represented in the reference set, thus classifying such fragments to its known broader taxonomic class or simply as "unknown". We compared the classification accuracy of TACOA with the latest intrinsic classifier PhyloPythia using 63 recently published complete genomes. For fragments of length 800 bp and 1 Kbp the overall accuracy of TACOA is higher than that obtained by PhyloPythia at all taxonomic ranks. For all fragment lengths, both methods achieved comparable high specificity results up to rank class and low false negative rates are also obtained. Conclusion: An accurate multi-class taxonomic classifier was developed for environmental genomic fragments. TACOA can predict with high reliability the taxonomic origin of genomic fragments as short as 800 bp. The proposed method is transparent, fast, accurate and the reference set can be easily updated as newly sequenced genomes become available. Moreover, the method demonstrated to be competitive when compared to the most current classifier PhyloPythia and has the advantage that it can be locally installed and the reference set can be kept up-to-date. Background:
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Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW. TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics. 2009;10(1):56.
Diaz, N. N., Krause, L., Goesmann, A., Niehaus, K., & Nattkemper, T. W. (2009). TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics, 10(1), 56. https://doi.org/10.1186/1471-2105-10-56
Diaz, Naryttza N., Krause, Lutz, Goesmann, Alexander, Niehaus, Karsten, and Nattkemper, Tim Wilhelm. 2009. “TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach”. BMC Bioinformatics 10 (1): 56.
Diaz, N. N., Krause, L., Goesmann, A., Niehaus, K., and Nattkemper, T. W. (2009). TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics 10, 56.
Diaz, N.N., et al., 2009. TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics, 10(1), p 56.
N.N. Diaz, et al., “TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach”, BMC Bioinformatics, vol. 10, 2009, pp. 56.
Diaz, N.N., Krause, L., Goesmann, A., Niehaus, K., Nattkemper, T.W.: TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics. 10, 56 (2009).
Diaz, Naryttza N., Krause, Lutz, Goesmann, Alexander, Niehaus, Karsten, and Nattkemper, Tim Wilhelm. “TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach”. BMC Bioinformatics 10.1 (2009): 56.
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Daten bereitgestellt von Europe PubMed Central.

Taxonomy based performance metrics for evaluating taxonomic assignment methods.
Chen CY, Tang SL, Chou ST., BMC Bioinformatics 20(1), 2019
PMID: 31185897
Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection.
Lambert C, Braxton C, Charlebois RL, Deyati A, Duncan P, La Neve F, Malicki HD, Ribrioux S, Rozelle DK, Michaels B, Sun W, Yang Z, Khan AS., Viruses 10(10), 2018
PMID: 30262776
Current Knowledge and Computational Techniques for Grapevine Meta-Omics Analysis.
Alaimo S, Marceca GP, Giugno R, Ferro A, Pulvirenti A., Front Plant Sci 8(), 2017
PMID: 29375610
Experimental metagenomics and ribosomal profiling of the human skin microbiome.
Ferretti P, Farina S, Cristofolini M, Girolomoni G, Tett A, Segata N., Exp Dermatol 26(3), 2017
PMID: 27623553
Origins and challenges of viral dark matter.
Krishnamurthy SR, Wang D., Virus Res 239(), 2017
PMID: 28192164
A clinician's guide to microbiome analysis.
Claesson MJ, Clooney AG, O'Toole PW., Nat Rev Gastroenterol Hepatol 14(10), 2017
PMID: 28790452
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities.
Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L., Mol Ecol 26(21), 2017
PMID: 28921802
CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.
Herath D, Tang SL, Tandon K, Ackland D, Halgamuge SK., BMC Bioinformatics 18(suppl 16), 2017
PMID: 29297295
Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.
Langenkämper D, Jakobi T, Feld D, Jelonek L, Goesmann A, Nattkemper TW., Front Genet 7(), 2016
PMID: 26904094
Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes.
Gupta A, Kumar S, Prasoodanan VP, Harish K, Sharma AK, Sharma VK., Front Microbiol 7(), 2016
PMID: 27148174
Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses.
Lam TT, Zhu H, Guan Y, Holmes EC., Annu Rev Genomics Hum Genet 17(), 2016
PMID: 27216777
Classification of metagenomics data at lower taxonomic level using a robust supervised classifier.
Hou T, Liu F, Liu Y, Zou QY, Zhang X, Wang K., Evol Bioinform Online 11(), 2015
PMID: 25673967
MBBC: an efficient approach for metagenomic binning based on clustering.
Wang Y, Hu H, Li X., BMC Bioinformatics 16(), 2015
PMID: 25652152
Exploiting topic modeling to boost metagenomic reads binning.
Zhang R, Cheng Z, Guan J, Zhou S., BMC Bioinformatics 16 Suppl 5(), 2015
PMID: 25859745
The human gut microbiome, a taxonomic conundrum.
Sankar SA, Lagier JC, Pontarotti P, Raoult D, Fournier PE., Syst Appl Microbiol 38(4), 2015
PMID: 25864640
CoMeta: classification of metagenomes using k-mers.
Kawulok J, Deorowicz S., PLoS One 10(4), 2015
PMID: 25884504
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.
Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I., Bioinform Biol Insights 9(), 2015
PMID: 25983555
FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples.
Lee J, Lee HT, Hong WY, Jang E, Kim J., J Microbiol Methods 115(), 2015
PMID: 26027543
Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data.
Aflitos SA, Severing E, Sanchez-Perez G, Peters S, de Jong H, de Ridder D., BMC Bioinformatics 16(), 2015
PMID: 26525298
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities.
Peabody MA, Van Rossum T, Lo R, Brinkman FS., BMC Bioinformatics 16(), 2015
PMID: 26537885
A New Unsupervised Binning Approach for Metagenomic Sequences Based on N-grams and Automatic Feature Weighting.
Liao R, Zhang R, Guan J, Zhou S., IEEE/ACM Trans Comput Biol Bioinform 11(1), 2014
PMID: 26355506
PhyloSift: phylogenetic analysis of genomes and metagenomes.
Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA., PeerJ 2(), 2014
PMID: 24482762
MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.
Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A., J Biotechnol 167(2), 2013
PMID: 23026555
A new vector for identification of prokaryotes and their variable-size genomes.
Hou T, Liu F, Lin CX, Li DY., Curr Microbiol 66(1), 2013
PMID: 23053493
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.
Klingenberg H, Aßhauer KP, Lingner T, Meinicke P., Bioinformatics 29(8), 2013
PMID: 23418187
The use of metagenomic approaches to analyze changes in microbial communities.
Neelakanta G, Sultana H., Microbiol Insights 6(), 2013
PMID: 24826073
Computational meta'omics for microbial community studies.
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C., Mol Syst Biol 9(), 2013
PMID: 23670539
Environmental bio-monitoring with high-throughput sequencing.
Wang J, McLenachan PA, Biggs PJ, Winder LH, Schoenfeld BI, Narayan VV, Phiri BJ, Lockhart PJ., Brief Bioinform 14(5), 2013
PMID: 23677899
High throughput sequencing methods and analysis for microbiome research.
Di Bella JM, Bao Y, Gloor GB, Burton JP, Reid G., J Microbiol Methods 95(3), 2013
PMID: 24029734
Analytical tools and databases for metagenomics in the next-generation sequencing era.
Kim M, Lee KH, Yoon SW, Kim BS, Chun J, Yi H., Genomics Inform 11(3), 2013
PMID: 24124405
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.
Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL., Nucleic Acids Res 40(1), 2012
PMID: 22102569
Metagenomics - a guide from sampling to data analysis.
Thomas T, Gilbert J, Meyer F., Microb Inform Exp 2(1), 2012
PMID: 22587947
Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community.
Radax R, Rattei T, Lanzen A, Bayer C, Rapp HT, Urich T, Schleper C., Environ Microbiol 14(5), 2012
PMID: 22364353
Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.
Sharma VK, Kumar N, Prakash T, Taylor TD., PLoS One 7(4), 2012
PMID: 22496776
Rapid identification of high-confidence taxonomic assignments for metagenomic data.
MacDonald NJ, Parks DH, Beiko RG., Nucleic Acids Res 40(14), 2012
PMID: 22532608
A comparative evaluation of sequence classification programs.
Bazinet AL, Cummings MP., BMC Bioinformatics 13(), 2012
PMID: 22574964
Functional assignment of metagenomic data: challenges and applications.
Prakash T, Taylor TD., Brief Bioinform 13(6), 2012
PMID: 22772835
Classification of metagenomic sequences: methods and challenges.
Mande SS, Mohammed MH, Ghosh TS., Brief Bioinform 13(6), 2012
PMID: 22962338
Separating metagenomic short reads into genomes via clustering.
Tanaseichuk O, Borneman J, Jiang T., Algorithms Mol Biol 7(1), 2012
PMID: 23009059
Analysis of composition-based metagenomic classification.
Higashi S, Barreto Ada M, Cantão ME, de Vasconcelos AT., BMC Genomics 13 Suppl 5(), 2012
PMID: 23095761
The binning of metagenomic contigs for microbial physiology of mixed cultures.
Strous M, Kraft B, Bisdorf R, Tegetmeyer HE., Front Microbiol 3(), 2012
PMID: 23227024
SPHINX--an algorithm for taxonomic binning of metagenomic sequences.
Mohammed MH, Ghosh TS, Singh NK, Mande SS., Bioinformatics 27(1), 2011
PMID: 21030462
Metagenomic analyses: past and future trends.
Simon C, Daniel R., Appl Environ Microbiol 77(4), 2011
PMID: 21169428
Mixture models for analysis of the taxonomic composition of metagenomes.
Meinicke P, Asshauer KP, Lingner T., Bioinformatics 27(12), 2011
PMID: 21546400
Taxonomic classification of metagenomic shotgun sequences with CARMA3.
Gerlach W, Stoye J., Nucleic Acids Res 39(14), 2011
PMID: 21586583
Microbial diversity in the midguts of field and lab-reared populations of the European corn borer Ostrinia nubilalis.
Belda E, Pedrola L, Peretó J, Martínez-Blanch JF, Montagud A, Navarro E, Urchueguía J, Ramón D, Moya A, Porcar M., PLoS One 6(6), 2011
PMID: 21738787
Classifying short genomic fragments from novel lineages using composition and homology.
Parks DH, MacDonald NJ, Beiko RG., BMC Bioinformatics 12(), 2011
PMID: 21827705
Eu-Detect: an algorithm for detecting eukaryotic sequences in metagenomic data sets.
Mohammed MH, Chadaram S, Komanduri D, Ghosh TS, Mande SS., J Biosci 36(4), 2011
PMID: 21857117
INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences.
Mohammed MH, Ghosh TS, Reddy RM, Reddy CV, Singh NK, Mande SS., BMC Genomics 12 Suppl 3(), 2011
PMID: 22369237
Accurate genome relative abundance estimation based on shotgun metagenomic reads.
Xia LC, Cram JA, Chen T, Fuhrman JA, Sun F., PLoS One 6(12), 2011
PMID: 22162995
From learning taxonomies to phylogenetic learning: integration of 16S rRNA gene data into FAME-based bacterial classification.
Slabbinck B, Waegeman W, Dawyndt P, De Vos P, De Baets B., BMC Bioinformatics 11(), 2010
PMID: 20113515
Treephyler: fast taxonomic profiling of metagenomes.
Schreiber F, Gumrich P, Daniel R, Meinicke P., Bioinformatics 26(7), 2010
PMID: 20172941
Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers.
Yang B, Peng Y, Leung HC, Yiu SM, Chen JC, Chin FY., BMC Bioinformatics 11 Suppl 2(), 2010
PMID: 20406503
Clustering metagenomic sequences with interpolated Markov models.
Kelley DR, Salzberg SL., BMC Bioinformatics 11(), 2010
PMID: 21044341
Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency.
Weng FC, Su CH, Hsu MT, Wang TY, Tsai HK, Wang D., BMC Bioinformatics 11(), 2010
PMID: 21083935
Achievements and new knowledge unraveled by metagenomic approaches.
Simon C, Daniel R., Appl Microbiol Biotechnol 85(2), 2009
PMID: 19760178
Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion.
Yung PY, Burke C, Lewis M, Egan S, Kjelleberg S, Thomas T., Nucleic Acids Res 37(21), 2009
PMID: 19767618
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.
Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J., BMC Bioinformatics 10(), 2009
PMID: 20021646

42 References

Daten bereitgestellt von Europe PubMed Central.

Shotgun sequencing of the human genome.
Venter JC, Adams MD, Sutton GG, Kerlavage AR, Smith HO, Hunkapiller M., Science 280(5369), 1998
PMID: 9644018
DNA sequencing with chain-terminating inhibitors.
Sanger F, Nicklen S, Coulson AR., Proc. Natl. Acad. Sci. U.S.A. 74(12), 1977
PMID: 271968
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM., Science 269(5223), 1995
PMID: 7542800
Community structure and metabolism through reconstruction of microbial genomes from the environment.
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF., Nature 428(6978), 2004
PMID: 14961025
Phylogenetic classification of short environmental DNA fragments.
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J., Nucleic Acids Res. 36(7), 2008
PMID: 18285365
Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor.
Krause L, Diaz NN, Edwards RA, Gartemann KH, Kromeke H, Neuweger H, Puhler A, Runte KJ, Schluter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18611419
Get the most out of your metagenome: computational analysis of environmental sequence data.
Raes J, Foerstner KU, Bork P., Curr. Opin. Microbiol. 10(5), 2007
PMID: 17936679
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental microbes
Abe T, Sugawara H, Kanaya S, Ikemura T., 2006
Accurate phylogenetic classification of variable-length DNA fragments.
McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I., Nat. Methods 4(1), 2006
PMID: 17179938
Binning sequences using very sparse labels within a metagenome.
Chan CK, Hsu AL, Halgamuge SK, Tang SL., BMC Bioinformatics 9(), 2008
PMID: 18442374
Compositional biases of bacterial genomes and evolutionary implications.
Karlin S, Mrazek J, Campbell AM., J. Bacteriol. 179(12), 1997
PMID: 9190805
Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA.
Campbell A, Mrazek J, Karlin S., Proc. Natl. Acad. Sci. U.S.A. 96(16), 1999
PMID: 10430917
Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier.
Sandberg R, Winberg G, Branden CI, Kaske A, Ernberg I, Coster J., Genome Res. 11(8), 2001
PMID: 11483581
MEGAN analysis of metagenomic data.
Huson DH, Auch AF, Qi J, Schuster SC., Genome Res. 17(3), 2007
PMID: 17255551
Genome sequencing in microfabricated high-density picolitre reactors.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM., Nature 437(7057), 2005
PMID: 16056220
The Pfam protein families database.
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18039703
Application of tetranucleotide frequencies for the assignment of genomic fragments.
Teeling H, Meyerdierks A, Bauer M, Amann R, Glockner FO., Environ. Microbiol. 6(9), 2004
PMID: 15305919
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.
Teeling H, Waldmann J, Lombardot T, Bauer M, Glockner FO., BMC Bioinformatics 5(), 2004
PMID: 15507136
Nearest Neighbor Pattern Classification
Cover T, Hart P., 1967

Hastie T, Tibshirami R, Friedman J., 2002
KNN-kernel density-based clustering for high-dimensional multivariate data
Tran TN, Wehrens R, Buydens LM., 2006
Instance-based concept learning from multiclass DNA microarray data.
Berrar D, Bradbury I, Dubitzky W., BMC Bioinformatics 7(), 2006
PMID: 16483361
In silico prediction of yeast deletion phenotypes.
Saha S, Heber S., Genet. Mol. Res. 5(1), 2006
PMID: 16755513
Using machine learning algorithms to guide rehabilitation planning for home care clients.
Zhu M, Zhang Z, Hirdes JP, Stolee P., BMC Med Inform Decis Mak 7(), 2007
PMID: 18096079
A vector space model for automatic indexing
Salton G, Wong A, Yang C., 1975
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V., Nucleic Acids Res. 33(17), 2005
PMID: 16214803
Database resources of the National Center for Biotechnology Information: 2002 update.
Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA., Nucleic Acids Res. 30(1), 2002
PMID: 11752242
Investigations of oligonucleotide usage variance within and between prokaryotes.
Bohlin J, Skjerve E, Ussery DW., PLoS Comput. Biol. 4(4), 2008
PMID: 18421372
Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications
Zhang SH, Ya-Zhi H., 2008
Ancient horizontal gene transfer.
Brown JR., Nat. Rev. Genet. 4(2), 2003
PMID: 12560809
Horizontal gene transfer in eukaryotic evolution.
Keeling PJ, Palmer JD., Nat. Rev. Genet. 9(8), 2008
PMID: 18591983
Horizontal gene transfer in prokaryotes: quantification and classification.
Koonin EV, Makarova KS, Aravind L., Annu. Rev. Microbiol. 55(), 2001
PMID: 11544372
DarkHorse: a method for genome-wide prediction of horizontal gene transfer.
Podell S, Gaasterland T., Genome Biol. 8(2), 2007
PMID: 17274820
The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum.
Ruepp A, Graml W, Santos-Martinez ML, Koretke KK, Volker C, Mewes HW, Frishman D, Stocker S, Lupas AN, Baumeister W., Nature 407(6803), 2000
PMID: 11029001
Horizontal gene transfer in bacterial and archaeal complete genomes.
Garcia-Vallve S, Romeu A, Palau J., Genome Res. 10(11), 2000
PMID: 11076857
Environments shape the nucleotide composition of genomes.
Foerstner KU, von Mering C, Hooper SD, Bork P., EMBO Rep. 6(12), 2005
PMID: 16200051
Assessing the accuracy of prediction algorithms for classification: an overview.
Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H., Bioinformatics 16(5), 2000
PMID: 10871264

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