Preprint Open Access

An interactive DNA barcode browser

Roderic D. M. Page


DataCite XML Export

<?xml version='1.0' encoding='utf-8'?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd">
  <identifier identifierType="DOI">10.5281/zenodo.4266482</identifier>
  <creators>
    <creator>
      <creatorName>Roderic D. M. Page</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-7101-9767</nameIdentifier>
      <affiliation>IBAHCM, MVLS, University of Glasgow</affiliation>
    </creator>
  </creators>
  <titles>
    <title>An interactive DNA barcode browser</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>DNA barcoding</subject>
    <subject>visualisation</subject>
    <subject>k-mer</subject>
    <subject>elasticsearch</subject>
    <subject>phylogeny</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-11-10</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Preprint</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4266482</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="Documents" resourceTypeGeneral="Software">https://dna-barcode-browser.herokuapp.com</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="Documents" resourceTypeGeneral="Software">https://github.com/rdmpage/dna-barcode-browser</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4266481</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;This paper describes an interactive web application to display DNA barcode data. It supports both query by sequence and query by geographic area. By using n-gram indexing of DNA sequences, and alignment-free phylogeny construction, the user can interactively explore DNA barcode data in real time.&lt;/p&gt;</description>
    <description descriptionType="Other">{"references": ["Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403\u2013410. DOI: 10.1016/S0022-2836(05)80360-2.", "Argim\u00f3n S, Abudahab K, Goater RJE, Fedosejev A, Bhai J, Glasner C, Feil EJ, Holden MTG, Yeats CA, Grundmann H, Spratt BG, Aanensen DM. 2016. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microbial Genomics, 2:e000093. DOI: 10.1099/mgen.0.000093.", "Edgar RC. 2004. Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Research 32:380\u2013385. DOI: 10.1093/nar/gkh180.", "Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61:1\u201310. DOI: 10.1016/0006-3207(92)91201-3.", "Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA. 2018. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 34:4121\u20134123. DOI: 10.1093/bioinformatics/bty407.", "Hajibabaei M, Singer GA. 2009. Googling DNA sequences on the World Wide Web. BMC Bioinformatics 10:S4. DOI: 10.1186/1471-2105-10-S14-S4.", "Maddison DR, Swofford DL, Maddison WP. 1997. Nexus: An Extensible File Format for Systematic Information. Systematic Biology 46:590\u2013621. DOI: 10.1093/sysbio/46.4.590.", "Meyer CP, Paulay G. 2005. DNA Barcoding: Error Rates Based on Comprehensive Sampling. PLOS Biology 3:e422. DOI: 10.1371/journal.pbio.0030422.", "Page R. 2015. Visualising geophylogenies in web maps using GeoJSON. PLoS currents 7.", "Ratnasingham S, Hebert PDN. 2013. A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System. PLOS ONE 8:e66213. DOI: 10.1371/journal.pone.0066213. Sahr K, White D, Kimerling AJ. 2003. Geodesic Discrete Global Grid Systems. Cartography and Geographic Information Science 30:121\u2013134. DOI: 10.1559/152304003100011090.", "Simonsen M, Mailund T, Pedersen CNS. 2008. Rapid Neighbour-Joining. In: Crandall KA, Lagergren J eds. Algorithms in Bioinformatics. Lecture Notes in Computer Science. Berlin, Heidelberg: Springer, 113\u2013122. DOI: 10.1007/978-3-540-87361-7_10.", "Stoeckle MY, Coffran C. 2013. TreeParser-Aided Klee Diagrams Display Taxonomic Clusters in DNA Barcode and Nuclear Gene Datasets. Scientific Reports 3:1\u20136. DOI: 10.1038/srep02635.", "Wieczorek J, Bloom D, Guralnick R, Blum S, D\u00f6ring M, Giovanni R, Robertson T, Vieglais D. 2012. Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLoS ONE 7:e29715. DOI: 10.1371/journal.pone.0029715.", "Yang K, Zhang L. 2008. Performance comparison between k -tuple distance and four model-based distances in phylogenetic tree reconstruction. Nucleic Acids Research 36:e33\u2013e33. DOI: 10.1093/nar/gkn075."]}</description>
  </descriptions>
</resource>
101
50
views
downloads
All versions This version
Views 101101
Downloads 5050
Data volume 12.2 MB12.2 MB
Unique views 8888
Unique downloads 4646

Share

Cite as