CiteULike | Further Information

• {"link"=>{"url"=>"http://www.citeulike.org/user/jmeppley/article/3658680"}, "post_time"=>"2016-01-08 19:26:42", "tag"=>["16s-rrna", "microbial-diversity", "tag-sequencing"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"jmeppley", "article_id"=>"3658680"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/Huub_odc/article/3658680"}, "post_time"=>"2009-02-04 08:10:39", "tag"=>["biodiversity", "metagenomics"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"Huub_odc", "article_id"=>"3658680"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/skembel/article/3658680"}, "post_time"=>"2008-11-23 21:20:41", "tag"=>["diversity", "microbial"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"skembel", "article_id"=>"3658680"}
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• {"link"=>{"url"=>"http://www.citeulike.org/user/djkt/article/3658680"}, "post_time"=>"2008-11-22 01:24:16", "tag"=>["metagenomics", "phylogenetics", "rna", "sequencing"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"djkt", "article_id"=>"3658680"}
• {"link"=>{"url"=>"http://www.citeulike.org/group/6072/article/3658680"}, "post_time"=>"2008-11-22 01:24:16", "tag"=>["16s", "metagenomics", "otu", "phylogenetics", "sequencing"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "group"=>"iSEEM", "group_id"=>"6072", "article_id"=>"3658680"}
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• {"link"=>{"url"=>"http://www.citeulike.org/user/druvus/article/3658680"}, "post_time"=>"2011-03-22 19:18:53", "tag"=>"metagenomics", "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"druvus", "article_id"=>"3658680"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/Zephyrus/article/3658680"}, "post_time"=>"2012-09-25 14:26:46", "tag"=>"kelvin-collab", "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"Zephyrus", "article_id"=>"3658680"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/migee/article/3658680"}, "post_time"=>"2010-06-16 21:37:17", "tag"=>"no-tag", "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"migee", "article_id"=>"3658680"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/jameswasmuth/article/3658680"}, "post_time"=>"2011-01-14 05:42:26", "tag"=>["microbiome", "next_generation"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"jameswasmuth", "article_id"=>"3658680"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/sconlan/article/3658680"}, "post_time"=>"2008-12-02 21:54:29", "tag"=>["16s", "454", "bacteria", "ecology", "environmental", "sequencing"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"sconlan", "article_id"=>"3658680"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/koyanagicl/article/3658680"}, "post_time"=>"2010-12-08 04:15:04", "tag"=>"microbiome", "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"koyanagicl", "article_id"=>"3658680"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/natldawson/article/3658680"}, "post_time"=>"2010-10-15 12:25:45", "tag"=>["gast", "phylogenetic_analysis"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"Pubmed Central", "url"=>"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577301/"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19023400"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19023400"}], "username"=>"natldawson", "article_id"=>"3658680"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/aarthiravikrishnan/article/14018928"}, "post_time"=>"2016-04-22 13:35:46", "tag"=>"mixed-bag", "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.1000255"}, {"type"=>"URL", "url"=>"http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2577301&tool=pmcentrez&rendertype=abstract"}], "username"=>"aarthiravikrishnan", "article_id"=>"14018928"}

Mendeley | Further Information

{"title"=>"Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Susan M.", "last_name"=>"Huse", "scopus_author_id"=>"14063451900"}, {"first_name"=>"Les", "last_name"=>"Dethlefsen", "scopus_author_id"=>"55980640700"}, {"first_name"=>"Julie A.", "last_name"=>"Huber", "scopus_author_id"=>"8734097400"}, {"first_name"=>"David Mark", "last_name"=>"Welch", "scopus_author_id"=>"7202920994"}, {"first_name"=>"David A.", "last_name"=>"Relman", "scopus_author_id"=>"7006375689"}, {"first_name"=>"Mitchell L.", "last_name"=>"Sogin", "scopus_author_id"=>"7006791887"}], "year"=>2008, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"57149093416", "pmid"=>"19023400", "pui"=>"352773666", "isbn"=>"1553-7404 (Electronic)", "scopus"=>"2-s2.0-57149093416", "doi"=>"10.1371/journal.pgen.1000255", "issn"=>"15537390"}, "id"=>"e421102b-d15d-39ef-b948-a33ba2600d98", "abstract"=>"Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA (SSU rRNA) genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary sequencing of full-length SSU rRNA. As with full-length rRNA surveys, each sequence read is a tag surrogate for a single microbe. However, rather than assigning taxonomy by creating gene trees de novo that include all experimental sequences and certain reference taxa, we compare the hypervariable region tags to an extensive database of rRNA sequences and assign taxonomy based on the best match in a Global Alignment for Sequence Taxonomy (GAST) process. The resulting taxonomic census provides information on both composition and diversity of the microbial community. To determine the effectiveness of using only hypervariable region tags for assessing microbial community membership, we compared the taxonomy assigned to the V3 and V6 hypervariable regions with the taxonomy assigned to full-length SSU rRNA sequences isolated from both the human gut and a deep-sea hydrothermal vent. The hypervariable region tags and full-length rRNA sequences provided equivalent taxonomy and measures of relative abundance of microbial communities, even for tags up to 15% divergent from their nearest reference match. The greater sampling depth per dollar afforded by massively parallel pyrosequencing reveals many more members of the \"rare biosphere\" than does capillary sequencing of the full-length gene. In addition, tag sequencing eliminates cloning bias and the sequences are short enough to be completely sequenced in a single read, maximizing the number of organisms sampled in a run while minimizing chimera formation. This technique allows the cost-effective exploration of changes in microbial community structure, including the rare biosphere, over space and time and can be applied immediately to initiatives, such as the Human Microbiome Project.", "link"=>"http://www.mendeley.com/research/exploring-microbial-diversity-taxonomy-using-ssu-rrna-hypervariable-tag-sequencing", "reader_count"=>1109, "reader_count_by_academic_status"=>{"Unspecified"=>20, "Professor > Associate Professor"=>86, "Librarian"=>1, "Researcher"=>290, "Student > Doctoral Student"=>52, "Student > Ph. D. Student"=>319, "Student > Postgraduate"=>34, "Student > Master"=>137, "Other"=>23, "Student > Bachelor"=>84, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>5, "Professor"=>50}, "reader_count_by_user_role"=>{"Unspecified"=>20, "Professor > Associate Professor"=>86, "Librarian"=>1, "Researcher"=>290, "Student > Doctoral Student"=>52, "Student > Ph. D. Student"=>319, "Student > Postgraduate"=>34, "Student > Master"=>137, "Other"=>23, "Student > Bachelor"=>84, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>5, "Professor"=>50}, "reader_count_by_subject_area"=>{"Unspecified"=>43, "Agricultural and Biological Sciences"=>725, "Arts and Humanities"=>1, "Veterinary Science and Veterinary Medicine"=>5, "Chemistry"=>16, "Computer Science"=>14, "Decision Sciences"=>1, "Earth and Planetary Sciences"=>24, "Engineering"=>22, "Environmental Science"=>74, "Biochemistry, Genetics and Molecular Biology"=>65, "Nursing and Health Professions"=>1, "Materials Science"=>1, "Mathematics"=>1, "Medicine and Dentistry"=>63, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>3, "Physics and Astronomy"=>4, "Psychology"=>3, "Social Sciences"=>6, "Immunology and Microbiology"=>34}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>63}, "Social Sciences"=>{"Social Sciences"=>6}, "Decision Sciences"=>{"Decision Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>4}, "Psychology"=>{"Psychology"=>3}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>43}, "Environmental Science"=>{"Environmental Science"=>74}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>3}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>22}, "Chemistry"=>{"Chemistry"=>16}, "Neuroscience"=>{"Neuroscience"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>24}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>34}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>725}, "Computer Science"=>{"Computer Science"=>14}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>65}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>5}}, "reader_count_by_country"=>{"United States"=>52, "Malaysia"=>2, "Portugal"=>3, "Russia"=>1, "Sweden"=>3, "Austria"=>1, "South Korea"=>1, "Netherlands"=>2, "Korea (South)"=>1, "Ireland"=>1, "China"=>2, "Brazil"=>8, "Slovenia"=>1, "France"=>5, "Nigeria"=>1, "Chile"=>2, "Argentina"=>1, "Uruguay"=>1, "Japan"=>2, "United Kingdom"=>7, "Ghana"=>1, "Switzerland"=>3, "Spain"=>4, "India"=>8, "New Zealand"=>1, "Canada"=>10, "Belgium"=>2, "Norway"=>1, "Finland"=>1, "Denmark"=>4, "South Africa"=>5, "Mexico"=>6, "Italy"=>3, "Israel"=>1, "Australia"=>1, "Germany"=>6, "Estonia"=>2, "Indonesia"=>1}, "group_count"=>49}

ORCID | Further Information

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• http://doi.org/10.1111/1462-2920.12092
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• http://doi.org/10.1111/j.1462-2920.2009.01941.x
• http://doi.org/10.1186/1471-2180-11-193
• http://doi.org/10.1128/AEM.00233-15

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• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/bda07687-2dc2-42ca-99ed-a578fc3b87a5", "title"=>"Link to companion paper", "body"=>"http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060280", "highlightedText"=>"''Dethlefsen et al.''\nhttp://plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000255#article1.front1.article-meta1.abstract2.p1", "isRemoved"=>false, "created"=>"2008-11-21T15:28:06Z", "lastModified"=>"2008-11-21T15:28:06Z", "creator"=>{"userId"=>"131543"}, "competingInterestStatement"=>{"creatorWasPrompted"=>false, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pgen.1000255", "state"=>"published", "journals"=>{"PLoSGenetics"=>{"journalKey"=>"PLoSGenetics", "eIssn"=>"1553-7404", "title"=>"PLOS Genetics"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2008-11-21T15:28:06Z", "replies"=>[]}
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• {"id"=>"342808744398295040", "text"=>"@Dr_Bik @MicrobesRock Yes. It can use any database, it's just search & taxonomic assignment that works differently. http://t.co/cJzghxkNOz", "created_at"=>"2013-06-07T01:02:28Z", "user"=>"JulesDeep", "user_name"=>"Julie Huber", "user_profile_image"=>"http://a0.twimg.com/profile_images/232018656/IMG_4188_normal.jpg"}
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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/915134"], "description"=>"<p>Assignment to genus and their relative abundances are distinctly similar for each of the three methods, V3 tag, V6 tag and full-length sequencing of SSU rRNA genes. Only sequences classified to the genus level are included. The tag sequencing approach, however, reveals many more rare taxa than does conventional full-length sequencing.</p>", "links"=>[], "tags"=>["taxonomic", "assignments", "sequences", "genus"], "article_id"=>585580, "categories"=>["Medicine", "Evolutionary Biology", "Biotechnology", "Ecology", "Microbiology", "Infectious Diseases", "Genetics", "Biological Sciences"], "users"=>["Susan M. Huse", "Les Dethlefsen", "Julie A. Huber", "David Mark Welch", "David A. Relman", "Mitchell L. Sogin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000255.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_taxonomic_assignments_for_human_gut_sequences_at_the_genus_level_/585580", "title"=>"Comparison of taxonomic assignments for human gut sequences at the genus level.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:31:19"}
• {"files"=>["https://ndownloader.figshare.com/files/915311"], "description"=>"<p>Treating the V3 and the V6 regions independently, we counted the number of assignments the GAST process made at each taxonomic rank and the number and percent of times those assignments were the same as the assignment given to the full-length source sequence. The second percent value is the rate at which the top BLAST match predicted the same assignment as the full-length source.</p>", "links"=>[], "tags"=>["taxonomic", "assignments", "full-length", "silico", "generated", "v3", "v6", "hypervariable"], "article_id"=>585754, "categories"=>["Medicine", "Evolutionary Biology", "Biotechnology", "Ecology", "Microbiology", "Infectious Diseases", "Genetics", "Biological Sciences"], "users"=>["Susan M. Huse", "Les Dethlefsen", "Julie A. Huber", "David Mark Welch", "David A. Relman", "Mitchell L. Sogin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000255.t002", "stats"=>{"downloads"=>5, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_taxonomic_assignments_using_full_length_and_in_silico_generated_V3_and_V6_hypervariable_region_tags_/585754", "title"=>"Comparison of taxonomic assignments using full-length and in silico generated V3 and V6 hypervariable region tags.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:32:23"}
• {"files"=>["https://ndownloader.figshare.com/files/915019"], "description"=>"<p>At each taxonomic level, the number of sequences from a particular taxon using one sequencing strategy (e.g., V6 tags) is plotted against the number of sequences from that same taxon using a second sequencing strategy (e.g., full-length SSU rRNA genes). For instance, classifying to the genus level, the Clostridial genus <i>Ruminococcus</i> occurred 186 times in the full-length SSU rRNA sequences and 19,332 times in the V6 tags. The order Clostridiales occurred 3,613 times in the full-length sequences, and 217,482 times in the V6 tags. <i>Note</i>: correlations are linear, although the axes use log scales for clarity. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000255#pgen-1000255-g003\" target=\"_blank\">Figure 3A</a> compares V6 tags with full-length sequences, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000255#pgen-1000255-g003\" target=\"_blank\">Figure 3B</a> compares V3 tags with full-length sequences, and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000255#pgen-1000255-g003\" target=\"_blank\">Figure 3C</a> compares V6 and V3 tags.</p>", "links"=>[], "tags"=>["taxonomic", "assignments", "sequences", "full-length", "ssu", "v3", "v6"], "article_id"=>585465, "categories"=>["Medicine", "Evolutionary Biology", "Biotechnology", "Ecology", "Microbiology", "Infectious Diseases", "Genetics", "Biological Sciences"], "users"=>["Susan M. Huse", "Les Dethlefsen", "Julie A. Huber", "David Mark Welch", "David A. Relman", "Mitchell L. Sogin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000255.g003", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_of_taxonomic_assignments_for_human_gut_sequences_based_on_full_length_SSU_rRNA_V3_and_V6_variable_regions_/585465", "title"=>"Correlation of taxonomic assignments for human gut sequences based on full-length SSU rRNA, V3 and V6 variable regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:30:41"}
• {"files"=>["https://ndownloader.figshare.com/files/915226"], "description"=>"<p>For GAST to accurately identify microbial taxa, the same tag sequence must not be present in different taxa: each tag should only have one taxonomic source. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000255#pgen-1000255-t001\" target=\"_blank\">Table 1</a> shows the percentage of hypervariable tags (V3 or V6) present in the RefSSU that map to single or multiple taxa. The results are displayed both as a percentage of tags and as a total number of tags.</p>", "links"=>[], "tags"=>["hypervariable", "tags", "refssu"], "article_id"=>585676, "categories"=>["Medicine", "Evolutionary Biology", "Biotechnology", "Ecology", "Microbiology", "Infectious Diseases", "Genetics", "Biological Sciences"], "users"=>["Susan M. Huse", "Les Dethlefsen", "Julie A. Huber", "David Mark Welch", "David A. Relman", "Mitchell L. Sogin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000255.t001", "stats"=>{"downloads"=>6, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percent_of_hypervariable_region_tags_from_the_RefSSU_database_that_map_to_one_or_more_taxa_/585676", "title"=>"Percent of hypervariable region tags from the RefSSU database that map to one or more taxa.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:31:58"}
• {"files"=>["https://ndownloader.figshare.com/files/915265"], "description"=>"<p>The percentages reported represent the frequency with which the top GAST match corresponds to the top BLAST match, the second best BLAST match, or any other BLAST match.</p>", "links"=>[], "tags"=>["ranks", "gast"], "article_id"=>585718, "categories"=>["Medicine", "Evolutionary Biology", "Biotechnology", "Ecology", "Microbiology", "Infectious Diseases", "Genetics", "Biological Sciences"], "users"=>["Susan M. Huse", "Les Dethlefsen", "Julie A. Huber", "David Mark Welch", "David A. Relman", "Mitchell L. Sogin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000255.t003", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_BLAST_ranks_for_top_GAST_hits_/585718", "title"=>"BLAST ranks for top GAST hits.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:32:11"}
• {"files"=>["https://ndownloader.figshare.com/files/914869"], "description"=>"<p>The percent of hypervariable region tags mapping to the same taxonomy as their source full-length SSU rRNA sequences is plotted as a function of the distance of the tags from their nearest GAST match in the reference database. Data from both the human gut and deep-sea vent for both hypervariable regions (V3 and V6) were combined to provide enough data points at greater distances. Only data points represented by a minimum of 5 tags were included. The GAST process consistently maps tags to the same taxonomy as their source for GAST distances up to 0.15 – a 15% divergence of the tag from its nearest match. Our combined datasets include only 61 tags (less than 0.4% of our tags) with a GAST distance > = 0.15, insufficient data to analyze the accuracy of the GAST process for these larger distances.</p>", "links"=>[], "tags"=>["gast", "taxonomic", "assignments", "distances"], "article_id"=>585316, "categories"=>["Medicine", "Evolutionary Biology", "Biotechnology", "Ecology", "Microbiology", "Infectious Diseases", "Genetics", "Biological Sciences"], "users"=>["Susan M. Huse", "Les Dethlefsen", "Julie A. Huber", "David Mark Welch", "David A. Relman", "Mitchell L. Sogin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000255.g001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accuracy_of_GAST_taxonomic_assignments_at_increasing_distances_from_the_reference_database_/585316", "title"=>"Accuracy of GAST taxonomic assignments at increasing distances from the reference database.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:29:43"}
• {"files"=>["https://ndownloader.figshare.com/files/914944"], "description"=>"<p>The Venn Diagram shows the extent of overlap between the V3, V6 and full-length sequencing of the human gut microbiome. The V3 tag sequencing found the most genera (116), the V6 found 103 genera, and full-length sequencing found only 43 genera.</p>", "links"=>[], "tags"=>["genera"], "article_id"=>585394, "categories"=>["Medicine", "Evolutionary Biology", "Biotechnology", "Ecology", "Microbiology", "Infectious Diseases", "Genetics", "Biological Sciences"], "users"=>["Susan M. Huse", "Les Dethlefsen", "Julie A. Huber", "David Mark Welch", "David A. Relman", "Mitchell L. Sogin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000255.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correspondence_of_genera_found_by_each_method_/585394", "title"=>"Correspondence of genera found by each method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:30:16"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime