publication . Article . 2015

CoMeta: classification of metagenomes using k-mers.

Jolanta Kawulok; Sebastian Deorowicz;
Open Access English
  • Published: 17 Apr 2015 Journal: PLoS ONE, volume 10, issue 1932-6203 (issn: 1932-6203, eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
Abstract
Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions. An important element of extracting the knowledge of the sample composition is to compare the extracted fragments of DNA with sequences derived from known organisms. In the presented paper, we introduce an algorithm called CoMeta (Classification of metagenomes), which assigns a query read (a DNA fragment) into one of the groups previously prepared by the user. Typically, this is one of the taxonomic rank (e.g., phylum, genus), however prepar...
Persistent Identifiers
Subjects
free text keywords: Q, R, Research Article, Science, Medicine, Taxonomic rank, Phylum, Search engine indexing, Biology, Artificial intelligence, business.industry, business, Read Classification, Metagenomics, Genomic databases, Natural language processing, computer.software_genre, computer, Reference genome, Sample composition, Genetics, lcsh:Medicine, lcsh:R, lcsh:Science, lcsh:Q
Communities
EGI Federation
Digital Humanities and Cultural Heritage
57 references, page 1 of 4

1 Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemistry & biology. 1998;5(10).

2 Pace NR, Stahl DA, Olsen GJ. Analyzing natural microbial populations by rRNA sequences. ASM News. 1985;51:4–12.

3 Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews. 2004;68(4):669–685. 10.1128/MMBR.68.4.669-685.2004 15590779 [OpenAIRE] [PubMed] [DOI]

4 Simon C, Daniel R. Metagenomic Analyses: Past and Future Trends. Applied and Environmental Microbiology. 2011;77(4):1153–1161. 10.1128/AEM.02345-10 21169428 [OpenAIRE] [PubMed] [DOI]

5 Committee on Metagenomics: Challenges and Functional Applications NRC. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. The National Academies Press; 2007.

6 Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, et al Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME Journal. 2010;4:1340–1351. 10.1038/ismej.2010.58 20445636 [OpenAIRE] [PubMed] [DOI]

7 Fierer N, Leff J, Adams B, Nielsen U, Bates S, Lauber C, et al Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(52). 10.1073/pnas.1215210110 [OpenAIRE] [DOI]

8 Abbai N, Govender A, Shaik R, Pillay B. Pyrosequence analysis of unamplified and whole genome amplified DNA from hydrocarbon-contaminated groundwater. Mol Biotechnol. 2011;50:39–48. 10.1007/s12033-011-9412-8 [OpenAIRE] [DOI]

9 Kennedy J, O’Leary ND, Kiran GS, Morrissey JP, O’Gara F, Selvin J, et al Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems. Journal of Applied Microbiology. 2011;111(4):787–799. 10.1111/j.1365-2672.2011.05106.x 21777355 [OpenAIRE] [PubMed] [DOI]

10 Gilbert J, Field D, Huang Y, Edwards R, Li W, Gilna P, et al Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE. 2008;3(8). 10.1371/journal.pone.0003042 [DOI]

11 Yergeau E, Lawrence JR, Waiser MJ, Korber DR, Greer CW. Metatranscriptomic analysis of the response of river biofilms to pharmaceutical products, using anonymous DNA microarrays. Applied and Environmental Microbiology. 2010;76(16):5432–5439. 10.1128/AEM.00873-10 20562274 [OpenAIRE] [PubMed] [DOI]

12 Rhee JK, Ahn DG, Kim YG, Oh JW. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Applied and Environmental Microbiology. 2005;71(2):817–825. 10.1128/AEM.71.2.817-825.2005 15691936 [OpenAIRE] [PubMed] [DOI]

13 Simon C, Wiezer A, Strittmatter AW, Daniel R. Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Applied and Environmental Microbiology. 2009;75(23):7519–7526. 10.1128/AEM.00946-09 19801459 [OpenAIRE] [PubMed] [DOI]

14 Heath C, Hu XPP, Cary SC, Cowan D. Identification of a novel alkaliphilic esterase active at low temperatures by screening a metagenomic library from antarctic desert soil. Applied and environmental microbiology. 2009;75(13):4657–4659. 10.1128/AEM.02597-08 19411411 [OpenAIRE] [PubMed] [DOI]

15 Nguyen NH, Maruset L, Uengwetwanit T, Mhuantong W, Harnpicharnchai P, Champreda V, et al Identification and characterization of a cellulase-encoding gene from the buffalo rumen metagenomic library. Bioscience, Biotechnology and Biochemistry. 2012;76(6):1075–1084.

57 references, page 1 of 4
Abstract
Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions. An important element of extracting the knowledge of the sample composition is to compare the extracted fragments of DNA with sequences derived from known organisms. In the presented paper, we introduce an algorithm called CoMeta (Classification of metagenomes), which assigns a query read (a DNA fragment) into one of the groups previously prepared by the user. Typically, this is one of the taxonomic rank (e.g., phylum, genus), however prepar...
Persistent Identifiers
Subjects
free text keywords: Q, R, Research Article, Science, Medicine, Taxonomic rank, Phylum, Search engine indexing, Biology, Artificial intelligence, business.industry, business, Read Classification, Metagenomics, Genomic databases, Natural language processing, computer.software_genre, computer, Reference genome, Sample composition, Genetics, lcsh:Medicine, lcsh:R, lcsh:Science, lcsh:Q
Communities
EGI Federation
Digital Humanities and Cultural Heritage
57 references, page 1 of 4

1 Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemistry & biology. 1998;5(10).

2 Pace NR, Stahl DA, Olsen GJ. Analyzing natural microbial populations by rRNA sequences. ASM News. 1985;51:4–12.

3 Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews. 2004;68(4):669–685. 10.1128/MMBR.68.4.669-685.2004 15590779 [OpenAIRE] [PubMed] [DOI]

4 Simon C, Daniel R. Metagenomic Analyses: Past and Future Trends. Applied and Environmental Microbiology. 2011;77(4):1153–1161. 10.1128/AEM.02345-10 21169428 [OpenAIRE] [PubMed] [DOI]

5 Committee on Metagenomics: Challenges and Functional Applications NRC. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. The National Academies Press; 2007.

6 Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, et al Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME Journal. 2010;4:1340–1351. 10.1038/ismej.2010.58 20445636 [OpenAIRE] [PubMed] [DOI]

7 Fierer N, Leff J, Adams B, Nielsen U, Bates S, Lauber C, et al Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(52). 10.1073/pnas.1215210110 [OpenAIRE] [DOI]

8 Abbai N, Govender A, Shaik R, Pillay B. Pyrosequence analysis of unamplified and whole genome amplified DNA from hydrocarbon-contaminated groundwater. Mol Biotechnol. 2011;50:39–48. 10.1007/s12033-011-9412-8 [OpenAIRE] [DOI]

9 Kennedy J, O’Leary ND, Kiran GS, Morrissey JP, O’Gara F, Selvin J, et al Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems. Journal of Applied Microbiology. 2011;111(4):787–799. 10.1111/j.1365-2672.2011.05106.x 21777355 [OpenAIRE] [PubMed] [DOI]

10 Gilbert J, Field D, Huang Y, Edwards R, Li W, Gilna P, et al Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE. 2008;3(8). 10.1371/journal.pone.0003042 [DOI]

11 Yergeau E, Lawrence JR, Waiser MJ, Korber DR, Greer CW. Metatranscriptomic analysis of the response of river biofilms to pharmaceutical products, using anonymous DNA microarrays. Applied and Environmental Microbiology. 2010;76(16):5432–5439. 10.1128/AEM.00873-10 20562274 [OpenAIRE] [PubMed] [DOI]

12 Rhee JK, Ahn DG, Kim YG, Oh JW. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Applied and Environmental Microbiology. 2005;71(2):817–825. 10.1128/AEM.71.2.817-825.2005 15691936 [OpenAIRE] [PubMed] [DOI]

13 Simon C, Wiezer A, Strittmatter AW, Daniel R. Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Applied and Environmental Microbiology. 2009;75(23):7519–7526. 10.1128/AEM.00946-09 19801459 [OpenAIRE] [PubMed] [DOI]

14 Heath C, Hu XPP, Cary SC, Cowan D. Identification of a novel alkaliphilic esterase active at low temperatures by screening a metagenomic library from antarctic desert soil. Applied and environmental microbiology. 2009;75(13):4657–4659. 10.1128/AEM.02597-08 19411411 [OpenAIRE] [PubMed] [DOI]

15 Nguyen NH, Maruset L, Uengwetwanit T, Mhuantong W, Harnpicharnchai P, Champreda V, et al Identification and characterization of a cellulase-encoding gene from the buffalo rumen metagenomic library. Bioscience, Biotechnology and Biochemistry. 2012;76(6):1075–1084.

57 references, page 1 of 4
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