A Scalable Method for Analysis and Display of DNA Sequences
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{"title"=>"A scalable method for analysis and display of DNA sequences", "type"=>"journal", "authors"=>[{"first_name"=>"Lawrence", "last_name"=>"Sirovich", "scopus_author_id"=>"7006836779"}, {"first_name"=>"Mark Y.", "last_name"=>"Stoeckle", "scopus_author_id"=>"57196678871"}, {"first_name"=>"Yu", "last_name"=>"Zhang", "scopus_author_id"=>"57192812344"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"355426551", "sgr"=>"70350036093", "doi"=>"10.1371/journal.pone.0007051", "scopus"=>"2-s2.0-70350036093", "isbn"=>"1932-6203", "pmid"=>"19798412"}, "id"=>"d0730038-557a-3f0e-b1ca-804008741480", "abstract"=>"BACKGROUND: Comparative DNA sequence analysis provides insight into evolution and helps construct a natural classification reflecting the Tree of Life. The growing numbers of organisms represented in DNA databases challenge tree-building techniques and the vertical hierarchical classification may obscure relationships among some groups. Approaches that can incorporate sequence data from large numbers of taxa and enable visualization of affinities across groups are desirable.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: Toward this end, we developed a procedure for extracting diagnostic patterns in the form of indicator vectors from DNA sequences of taxonomic groups. In the present instance the indicator vectors were derived from mitochondrial cytochrome c oxidase I (COI) sequences of those groups and further analyzed on this basis. In the first example, indicator vectors for birds, fish, and butterflies were constructed from a training set of COI sequences, then correlations with test sequences not used to construct the indicator vector were determined. In all cases, correlation with the indicator vector correctly assigned test sequences to their proper group. In the second example, this approach was explored at the species level within the bird grouping; this also gave correct assignment, suggesting the possibility of automated procedures for classification at various taxonomic levels. A false-color matrix of vector correlations displayed affinities among species consistent with higher-order taxonomy.\\n\\nCONCLUSIONS/SIGNIFICANCE: The indicator vectors preserved DNA character information and provided quantitative measures of correlations among taxonomic groups. This method is scalable to the largest datasets envisioned in this field, provides a visually-intuitive display that captures relational affinities derived from sequence data across a diversity of life forms, and is potentially a useful complement to current tree-building techniques for studying evolutionary processes based on DNA sequence data.", "link"=>"http://www.mendeley.com/research/scalable-method-analysis-display-dna-sequences", "reader_count"=>86, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>35, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>4, "Student > Master"=>5, "Other"=>3, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>35, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>4, "Student > Master"=>5, "Other"=>3, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>6, "Mathematics"=>1, "Agricultural and Biological Sciences"=>64, "Medicine and Dentistry"=>3, "Business, Management and Accounting"=>1, "Chemistry"=>1, "Computer Science"=>3, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>64}, "Computer Science"=>{"Computer Science"=>3}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Colombia"=>1, "Argentina"=>1, "United States"=>3, "United Kingdom"=>2, "India"=>1, "Spain"=>1, "Canada"=>1, "Netherlands"=>1, "Belgium"=>1, "Brazil"=>3, "Mexico"=>1, "Chile"=>1, "Peru"=>1, "Germany"=>2}, "group_count"=>6}

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/881196"], "description"=>"<p>A false-color map depicting correlations among indicator vectors , , and for COI sequences of birds, fish, and butterflies, respectively, is shown. The numerical correlation values are indicated.</p>", "links"=>[], "tags"=>["group-level"], "article_id"=>551659, "categories"=>["Infectious Diseases", "Evolutionary Biology", "Genetics"], "users"=>["Lawrence Sirovich", "Mark Y. Stoeckle", "Yu Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0007051.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_among_group_level_indicator_vectors_/551659", "title"=>"Correlation among group-level indicator vectors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 04:22:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/881277"], "description"=>"<p>False-color map of 4,332 COI test sequences compared to the indicator vectors depicted in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007051#pone-0007051-g001\" target=\"_blank\">Figure 1</a>. In all cases, the test sequences showed highest affinity with their respective group vector.</p>", "links"=>[], "tags"=>["sequences", "group-level"], "article_id"=>551738, "categories"=>["Infectious Diseases", "Evolutionary Biology", "Genetics"], "users"=>["Lawrence Sirovich", "Mark Y. Stoeckle", "Yu Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0007051.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_of_test_sequences_with_group_level_indicator_vectors_/551738", "title"=>"Correlation of test sequences with group-level indicator vectors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 04:22:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/881378"], "description"=>"<p>A false color map depicting correlations among indicator vectors for 122 species of North American birds is shown in (A) where order is alphabetical by species name. Blocks of high correlation on the diagonal reflected affinity among species within genera. The large squares of highly-correlated birds in the upper left hand corner indicated close affinities among species in several genera of ducks and geese (<i>Aix, Anas, Athya, Branta, Bucephala</i>). In (B) the ordering follows established taxonomy, reflecting phylogenetic relationships <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007051#pone.0007051-1\" target=\"_blank\">[13]</a>.</p>", "links"=>[], "tags"=>["species-level"], "article_id"=>551841, "categories"=>["Infectious Diseases", "Evolutionary Biology", "Genetics"], "users"=>["Lawrence Sirovich", "Mark Y. Stoeckle", "Yu Zhang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0007051.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_among_species_level_indicator_vectors_/551841", "title"=>"Correlation among species-level indicator vectors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 04:23:22"}

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Relative Metric

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