Frequency Matrix Approach Demonstrates High Sequence Quality in Avian BARCODEs and Highlights Cryptic Pseudogenes
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{"title"=>"Frequency matrix approach demonstrates high sequence quality in Avian BARCODEs and highlights cryptic pseudogenes", "type"=>"journal", "authors"=>[{"first_name"=>"Mark Y.", "last_name"=>"Stoeckle", "scopus_author_id"=>"57196678871"}, {"first_name"=>"Kevin C.R.", "last_name"=>"Kerr", "scopus_author_id"=>"16833371800"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"365513899", "scopus"=>"2-s2.0-84865412170", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22952842", "sgr"=>"84865412170", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0043992"}, "id"=>"392aeda8-219f-3427-b944-426d079a6c83", "abstract"=>"The accuracy of DNA barcode databases is critical for research and practical applications. Here we apply a frequency matrix to assess sequencing errors in a very large set of avian BARCODEs. Using 11,000 sequences from 2,700 bird species, we show most avian cytochrome c oxidase I (COI) nucleotide and amino acid sequences vary within a narrow range. Except for third codon positions, nearly all (96%) sites were highly conserved or limited to two nucleotides or two amino acids. A large number of positions had very low frequency variants present in single individuals of a species; these were strongly concentrated at the ends of the barcode segment, consistent with sequencing error. In addition, a small fraction (0.1%) of BARCODEs had multiple very low frequency variants shared among individuals of a species; these were found to represent overlooked cryptic pseudogenes lacking stop codons. The calculated upper limit of sequencing error was 8 × 10(-5) errors/nucleotide, which was relatively high for direct Sanger sequencing of amplified DNA, but unlikely to compromise species identification. Our results confirm the high quality of the avian BARCODE database and demonstrate significant quality improvement in avian COI records deposited in GenBank over the past decade. This approach has potential application for genetic database quality control, discovery of cryptic pseudogenes, and studies of low-level genetic variation.", "link"=>"http://www.mendeley.com/research/frequency-matrix-approach-demonstrates-high-sequence-quality-avian-barcodes-highlights-cryptic-pseud", "reader_count"=>41, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>9, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>9, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>33, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>33}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Mexico"=>1, "United Kingdom"=>1, "France"=>2, "Switzerland"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/585920"], "description"=>"<p>Distribution of very low frequency (VLF) variants across barcode segment. A) Nucleotide. B) Amino acid.</p>", "links"=>[], "tags"=>["variants", "barcode", "amino"], "article_id"=>256416, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Mark Y. Stoeckle", "Kevin C. R. Kerr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043992.g003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_very_low_frequency_VLF_variants_across_barcode_segment_A_Nucleotide_B_Amino_acid_/256416", "title"=>"Distribution of very low frequency (VLF) variants across barcode segment. A) Nucleotide. B) Amino acid.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:46:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/586165"], "description"=>"<p>A) <i>Cnemotriccus fuscatus</i>. Nucleotides underlying amino acid VLFs for all <i>C. fuscatus</i> GenBank records are shown (underlined are BARCODEs); complete mitochondrial genome sequence AY596278 is at bottom. Representative trace files show double peaks at VLF positions highlighted in yellow (BARCODE numbering differs by 2 from forward trace files). B) <i>B. canadensis</i>. Trace files for outlier BARCODEs display double peaks at VLF sites. The GenBank fasta file sequence for these records is shown with the VLF nucleotide highlighted in yellow and the sequence from a representative conspecific BARCODE lacking VLFs below.</p>", "links"=>[], "tags"=>["barcodes", "amino", "vlfs", "co-amplified"], "article_id"=>256652, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Mark Y. Stoeckle", "Kevin C. R. Kerr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043992.g005", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Additional_BARCODEs_with_multiple_shared_amino_acid_VLFs_reflect_co_amplified_pseudogenes_/256652", "title"=>"Additional BARCODEs with multiple shared amino acid VLFs reflect co-amplified pseudogenes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:50:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/585803"], "description"=>"<p>Bars below ranked histograms show conservation of positions: 100% (black), <100% and >99.9% (red), and <99.9% (gray).</p>", "links"=>[], "tags"=>["nucleotide", "amino", "positions", "avian"], "article_id"=>256297, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Mark Y. Stoeckle", "Kevin C. R. Kerr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043992.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variant_nucleotide_and_amino_acid_positions_among_11_333_avian_BARCODEs_/256297", "title"=>"Variant nucleotide and amino acid positions among 11,333 avian BARCODEs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:44:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/586615"], "description"=>"<p>Number of conserved and highly conserved positions and average number and range of differences from the 1<sup>st</sup> modal sequence are shown. Percentages are given in parentheses.</p>", "links"=>[], "tags"=>["nucleotide", "amino", "positions", "avian"], "article_id"=>257109, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Mark Y. Stoeckle", "Kevin C. R. Kerr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043992.t001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conservation_of_nucleotide_and_amino_acid_positions_in_avian_BARCODEs_/257109", "title"=>"Conservation of nucleotide and amino acid positions in avian BARCODEs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-27 01:58:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/586331"], "description"=>"<p>Bars indicate 95% confidence intervals.</p>", "links"=>[], "tags"=>["singleton", "nucleotide", "vlfs", "avian", "barcode", "non-barcode", "coi", "records", "deposited", "genbank", "january", "intervals", "2000", "december", "2004", "2005", "june", "2007", "july", "2009", "2010", "april", "2012"], "article_id"=>256774, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Mark Y. Stoeckle", "Kevin C. R. Kerr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043992.g006", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prevalence_of_singleton_nucleotide_VLFs_in_avian_BARCODE_and_non_BARCODE_COI_records_deposited_in_GenBank_since_January_1_2000_Intervals_are_January_1_2000_to_December_31_2004_2000_8211_04_January_1_2005_to_June_30_2007_2005_8211_07_July_1_2007_to_Decemb/256774", "title"=>"Prevalence of singleton nucleotide VLFs in avian BARCODE and non-BARCODE COI records deposited in GenBank since January 1, 2000. Intervals are January 1, 2000 to December 31, 2004 (2000–04); January 1, 2005 to June 30, 2007 (2005–07); July 1, 2007 to December 31, 2009 (2007–09), and January 1, 2010 to April 30, 2012 (2010–12).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:52:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/586575"], "description"=>"<p>The subset of shared VLFs contained in pseudogenes is shown at bottom. The concordance of sequences with nucleotide (nt) and amino acid (aa) VLFs is shown at right.</p>", "links"=>[], "tags"=>["variants", "avian"], "article_id"=>257070, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Mark Y. Stoeckle", "Kevin C. R. Kerr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043992.t002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Singleton_and_shared_very_low_frequency_VLF_variants_in_avian_BARCODEs_/257070", "title"=>"Singleton and shared very low frequency (VLF) variants in avian BARCODEs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-27 01:57:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/586446"], "description"=>"<p>Gray bars indicate sequence alignment relative to 648 bp barcode region, VLFs are in red, and blanks indicate ambiguous positions. VLFs were concentrated at the 5′ or 3′ terminus, consistent with sequencing error, except for <i>C. frugilegus</i> EF515782, which appeared to be a pseudogene (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043992#pone.0043992.s003\" target=\"_blank\">Fig. S3</a>).</p>", "links"=>[], "tags"=>["nucleotide", "singleton", "genbank", "accession", "vlfs"], "article_id"=>256939, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Mark Y. Stoeckle", "Kevin C. R. Kerr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043992.g007", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_BARCODEs_with_four_or_more_nucleotide_singleton_VLFs_Species_name_GenBank_accession_number_and_number_of_VLFs_are_shown_/256939", "title"=>"BARCODEs with four or more nucleotide singleton VLFs. Species name, GenBank accession number, and number of VLFs are shown.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:55:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/586043"], "description"=>"<p>Schematic shows positions of amino acid VLFs in barcode segment for <i>E. alnorum</i> BARCODEs with GenBank accession numbers as indicated. Representative trace files shown below display a double peak underlying the 5′ amino acid VLF and an overlooked single base insertion near nucleotide position 470. The GenBANK fasta file sequence corresponding to the insertion site is shown below the traces with the unrecorded nucleotide in yellow.</p>", "links"=>[], "tags"=>["barcodes", "co-amplified"], "article_id"=>256540, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Mark Y. Stoeckle", "Kevin C. R. Kerr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043992.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Empidonax_alnorum_BARCODEs_represent_a_co_amplified_pseudogene_/256540", "title"=>"<i>Empidonax alnorum</i> BARCODEs represent a co-amplified pseudogene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:49:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/585694"], "description"=>"<p>Representation of avian orders and families in BARCODE library.</p>", "links"=>[], "tags"=>["avian", "orders", "barcode"], "article_id"=>256188, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Mark Y. Stoeckle", "Kevin C. R. Kerr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043992.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representation_of_avian_orders_and_families_in_BARCODE_library_/256188", "title"=>"Representation of avian orders and families in BARCODE library.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:43:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/308675", "https://ndownloader.figshare.com/files/308702", "https://ndownloader.figshare.com/files/308744", "https://ndownloader.figshare.com/files/308806", "https://ndownloader.figshare.com/files/309334"], "description"=>"<div><p>The accuracy of DNA barcode databases is critical for research and practical applications. Here we apply a frequency matrix to assess sequencing errors in a very large set of avian BARCODEs. Using 11,000 sequences from 2,700 bird species, we show most avian cytochrome c oxidase I (COI) nucleotide and amino acid sequences vary within a narrow range. Except for third codon positions, nearly all (96%) sites were highly conserved or limited to two nucleotides or two amino acids. A large number of positions had very low frequency variants present in single individuals of a species; these were strongly concentrated at the ends of the barcode segment, consistent with sequencing error. In addition, a small fraction (0.1%) of BARCODEs had multiple very low frequency variants shared among individuals of a species; these were found to represent overlooked cryptic pseudogenes lacking stop codons. The calculated upper limit of sequencing error was 8×10<sup>−5</sup> errors/nucleotide, which was relatively high for direct Sanger sequencing of amplified DNA, but unlikely to compromise species identification. Our results confirm the high quality of the avian BARCODE database and demonstrate significant quality improvement in avian COI records deposited in GenBank over the past decade. This approach has potential application for genetic database quality control, discovery of cryptic pseudogenes, and studies of low-level genetic variation.</p> </div>", "links"=>[], "tags"=>["matrix", "demonstrates", "avian", "barcodes", "highlights", "cryptic", "pseudogenes"], "article_id"=>120895, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Mark Y. Stoeckle", "Kevin C. R. Kerr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0043992.s001", "https://dx.doi.org/10.1371/journal.pone.0043992.s002", "https://dx.doi.org/10.1371/journal.pone.0043992.s003", "https://dx.doi.org/10.1371/journal.pone.0043992.s004", "https://dx.doi.org/10.1371/journal.pone.0043992.s005"], "stats"=>{"downloads"=>3, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Frequency_Matrix_Approach_Demonstrates_High_Sequence_Quality_in_Avian_BARCODEs_and_Highlights_Cryptic_Pseudogenes/120895", "title"=>"Frequency Matrix Approach Demonstrates High Sequence Quality in Avian BARCODEs and Highlights Cryptic Pseudogenes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-08-27 00:14:55"}

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  • {"unique-ip"=>"6", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"2", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"0", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[375, 629, 760, 889, 1000, 1110, 1203, 1298, 1399, 1492, 1603, 1699, 1774, 1855, 1918, 1998, 2062, 2152, 2227, 2312, 2378, 2461, 2528, 2600, 2664]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[333, 576, 707, 814, 908, 1004, 1104, 1197, 1280, 1370, 1449, 1531, 1603, 1673, 1742, 1817, 1886, 1954, 2025, 2098, 2171, 2234, 2304, 2365, 2431]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[324, 551, 679, 782, 879, 971, 1064, 1154, 1245, 1328, 1406, 1476, 1541, 1617, 1683, 1754, 1818, 1893, 1962, 2025, 2092, 2164, 2227, 2294, 2355]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[331, 557, 677, 777, 868, 960, 1050, 1136, 1223, 1307, 1390, 1466, 1536, 1603, 1673, 1741, 1814, 1889, 1954, 2028, 2096, 2164, 2233, 2305, 2362]}]}
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