Preprint Open Access

An interactive DNA barcode browser

Roderic D. M. Page

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.

Files (243.5 kB)
Name Size
An interactive DNA barcode browser.pdf
md5:c3f18952039dc6f9e48567d17dcd9b6f 		243.5 kB Download

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403–410. DOI: 10.1016/S0022-2836(05)80360-2.

  • Argimón 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 32:380–385. DOI: 10.1093/nar/gkh180.

  • Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61:1–10. 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 34:4121–4123. 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 46:590–621. 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 30:121–134. 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, 113–122. 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 3:1–6. DOI: 10.1038/srep02635.

  • Wieczorek J, Bloom D, Guralnick R, Blum S, Döring 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–e33. DOI: 10.1093/nar/gkn075.

103
52
views
downloads
All versions This version
Views 103103
Downloads 5252
Data volume 12.7 MB12.7 MB
Unique views 9090
Unique downloads 4848
More info on how stats are collected.
Indexed in
Publication date:
November 10, 2020
DOI:
10.5281/zenodo.4266482

Zenodo DOI Badge

DOI 

10.5281/zenodo.4266482

Markdown 

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4266482.svg)](https://doi.org/10.5281/zenodo.4266482)

reStructedText 

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4266482.svg
   :target: https://doi.org/10.5281/zenodo.4266482

HTML 

<a href="https://doi.org/10.5281/zenodo.4266482"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4266482.svg" alt="DOI"></a>

Image URL 

https://zenodo.org/badge/DOI/10.5281/zenodo.4266482.svg

Target URL 

https://doi.org/10.5281/zenodo.4266482

Keyword(s):
DNA barcoding visualisation k-mer elasticsearch phylogeny
Related identifiers:
Documents
License (for files):
Creative Commons Attribution 4.0 International

Versions

Version 1 10.5281/zenodo.4266482 Nov 10, 2020
Cite all versions? You can cite all versions by using the DOI 10.5281/zenodo.4266481. This DOI represents all versions, and will always resolve to the latest one. Read more.

Share

Cite as

Export