Published November 10, 2020
| Version v1
Preprint
Open
An interactive DNA barcode browser
Description
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
An interactive DNA barcode browser.pdf
Files
(243.5 kB)
Name | Size | Download all |
---|---|---|
md5:c3f18952039dc6f9e48567d17dcd9b6f
|
243.5 kB | Preview Download |
Additional details
Related works
- Documents
- Software: https://dna-barcode-browser.herokuapp.com (URL)
- Software: https://github.com/rdmpage/dna-barcode-browser (URL)
References
- 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.