A Primer on Metagenomics
Publication Date
February 26, 2010
Journal
PLOS Computational Biology
Authors
John C. Wooley, Adam Godzik & Iddo Friedberg
Volume
6
Issue
2
Pages
e1000667
DOI
https://dx.plos.org/10.1371/journal.pcbi.1000667
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1000667
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/20195499
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829047
Europe PMC
http://europepmc.org/abstract/MED/20195499
Web of Science
000275260000004
Scopus
77649200259
Mendeley
http://www.mendeley.com/research/primer-metagenomics
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/861206"], "description"=>"a<p>Based on the GA IIx. See full specifications at: <a href=\"http://www.illumina.com/systems/genome_analyzer.ilmn\" target=\"_blank\">http://www.illumina.com/systems/genome_analyzer.ilmn</a>.</p>b<p>mp, mate pair; frag, fragment. See <a href=\"https://products.appliedbiosystems.com/\" target=\"_blank\">https://products.appliedbiosystems.com/</a> SOLiD 3 Plus System.</p>c<p>See: <a href=\"http://www.helicosbio.com/Products/HelicosregGeneticAnalysisSystem/HeliScopetradeSequencer/tabid/87/Default.aspx\" target=\"_blank\">http://www.helicosbio.com/Products/HelicosregGeneticAnalysisSystem/HeliScopetradeSequencer/tabid/87/Default.aspx</a>.</p>", "links"=>[], "tags"=>["sequencing", "taken"], "article_id"=>531667, "categories"=>["Infectious Diseases", "Microbiology", "Virology", "Biological Sciences"], "users"=>["John C. Wooley", "Adam Godzik", "Iddo Friedberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000667.t001", "stats"=>{"downloads"=>4, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_different_sequencing_technologies_taken_from_34_/531667", "title"=>"Comparison of different sequencing technologies, taken from [34].", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 02:29:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/861175"], "description"=>"<p>The information contained in different lengths of genomic DNA.</p>", "links"=>[], "tags"=>["contained", "lengths", "genomic"], "article_id"=>531636, "categories"=>["Infectious Diseases", "Microbiology", "Virology", "Biological Sciences"], "users"=>["John C. Wooley", "Adam Godzik", "Iddo Friedberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000667.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_information_contained_in_different_lengths_of_genomic_DNA_/531636", "title"=>"The information contained in different lengths of genomic DNA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 02:29:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/860881"], "description"=>"<p>Single stranded DNA template is first hybridized with the sequencing primer and mixed with the enzymes along with the two substrates adenosine 5′-phosphosulfate (APS) and luciferin. In each cycle, (1) one of the four nucleotides (dTTPi, in this case) is then added to the reaction. (2) If the nucleotide is complementary to the base in the template strand then the DNA polymerase incorporates it into the growing strand. (3) Pyrophosphate (PPi)—in an amount equal in molarity to that of the incorporated nucleotide—is released and converted to ATP by sulfurylase in the presence of APS. (4) ATP then serves as a substrate to luciferase, causing a light reaction. Photon emission is in equimolar quanta to the amount of nucleotide incorporated in a given cycle. (5) The excess nucleotides are degraded by apyrase.</p>", "links"=>[], "tags"=>["computational biology/genomics", "computational biology/metagenomics", "computational biology/sequence motif analysis", "microbiology", "microbiology/environmental microbiology", "microbiology/microbial evolution and genomics"], "article_id"=>531339, "categories"=>["Infectious Diseases", "Microbiology", "Virology", "Biological Sciences"], "users"=>["John C. Wooley", "Adam Godzik", "Iddo Friedberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000667.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pyrosequencing_/531339", "title"=>"Pyrosequencing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:27:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/861090"], "description"=>"<p>Green, most or all species have been sampled; blue, this habitat has not been exhaustively sampled; red, species rich habitat, only a small fraction has been sampled.</p>", "links"=>[], "tags"=>["computational biology/genomics", "computational biology/metagenomics", "computational biology/sequence motif analysis", "microbiology", "microbiology/environmental microbiology", "microbiology/microbial evolution and genomics"], "article_id"=>531545, "categories"=>["Infectious Diseases", "Microbiology", "Virology", "Biological Sciences"], "users"=>["John C. Wooley", "Adam Godzik", "Iddo Friedberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000667.g004", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rarefaction_curves_/531545", "title"=>"Rarefaction curves.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:29:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/860975"], "description"=>"<p>(A–C) Hamiltonian. (A) A sequence with overlapping reads; (B) Each read is represented as a vertex, with edges connecting the overlapping vertices; (C) the assembly solution is a Hamiltonian path (all vertices are visited, no vertex is visited more than once) through the resulting graph; (D) For short reads assembly, each vertex is a <i>k</i>-mer (or a hashed collection of <i>k</i>-mers), and the reads are threaded between vertices as edges. The solution is a Eulerian path, where each edge is visited once. Repeats are merged into a single edge. For detailed algorithms see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000667#pcbi.1000667-Pevzner1\" target=\"_blank\">[49]</a>, <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000667#pcbi.1000667-Chaisson1\" target=\"_blank\">[50]</a>, <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000667#pcbi.1000667-Zerbino1\" target=\"_blank\">[53]</a>–<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000667#pcbi.1000667-Warren1\" target=\"_blank\">[55]</a>.</p>", "links"=>[], "tags"=>["computational biology/genomics", "computational biology/metagenomics", "computational biology/sequence motif analysis", "microbiology", "microbiology/environmental microbiology", "microbiology/microbial evolution and genomics"], "article_id"=>531429, "categories"=>["Infectious Diseases", "Microbiology", "Virology", "Biological Sciences"], "users"=>["John C. Wooley", "Adam Godzik", "Iddo Friedberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000667.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fragment_assembly_/531429", "title"=>"Fragment assembly.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:28:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/860794"], "description"=>"<p>(A) Sampling from habitat; (B) filtering particles, typically by size; (C) DNA extraction and lysis; (D) cloning and library; (E) sequence the clones; (F) sequence assembly.</p>", "links"=>[], "tags"=>["shotgun", "sequencing"], "article_id"=>531251, "categories"=>["Infectious Diseases", "Microbiology", "Virology", "Biological Sciences"], "users"=>["John C. Wooley", "Adam Godzik", "Iddo Friedberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000667.g001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Environmental_Shotgun_Sequencing_ESS_/531251", "title"=>"Environmental Shotgun Sequencing (ESS).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 02:27:26"}

PMC Usage Stats | Further Information

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