DNA barcode goes two-dimensions: DNA QR code web server.

PloS One
Chang LiuShi-lin Chen

Abstract

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been ca...Continue Reading

References

Dec 20, 2002·Bioinformatics·Xin ChenJohn Tromp
Mar 5, 2003·Proceedings. Biological Sciences·Paul D N HebertJeremy R deWaard
Sep 4, 2003·Proceedings. Biological Sciences·Paul D N HebertJeremy R deWaard
Jun 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·W John KressDaniel H Janzen
Oct 13, 2007·Science·Elizabeth Pennisi
Feb 8, 2008·Nature·Heidi Ledford
Feb 9, 2008·Proceedings of the National Academy of Sciences of the United States of America·Renaud LahayeVincent Savolainen
Feb 20, 2008·Computer Methods and Programs in Biomedicine·N Pradeep KumarP Jambulingam
May 19, 2009·Bioinformatics·Marty C BrandonPierre Baldi
Aug 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·UNKNOWN CBOL Plant Working Group
Nov 6, 2009·International Journal of Bioinformatics Research and Applications·Taysir H A SolimanM A El Sharkawy
Jul 8, 2010·Bioinformatics·Waibhav TembeEdward Suh
Jan 27, 2011·Nucleic Acids Research·Congmao Wang, Dabing Zhang
Jun 4, 2011·PloS One·Peter M HollingsworthDamon P Little
Nov 22, 2011·Proceedings of the National Academy of Sciences of the United States of America·UNKNOWN China Plant BOL GroupGuang-Wen Duan

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Citations

Jan 25, 2013·Journal of the American Medical Informatics Association : JAMIA·Matthias Samwald, Klaus-Peter Adlassnig
Aug 3, 2013·The Journal of Surgical Research·Jennifer L DixonHarry T Papaconstantinou
Jan 8, 2016·Scientific Reports·Jianping HanShilin Chen
Apr 1, 2015·The Journal of Nursing Education·Jennifer BellotMary Wang
Nov 19, 2015·Acta Pharmaceutica Sinica. B·Lili WangShilin Chen
Jun 20, 2015·Evidence-based Complementary and Alternative Medicine : ECAM·Yong CaiYitao Wang
Jun 7, 2015·Critical Reviews in Food Science and Nutrition·Javier Sanz-ValeroJuan M Santos Gago
Apr 23, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ravi P More, Hemant J Purohit
Dec 19, 2016·BioData Mining·Ravi Prabhakar MoreHemant J Purohit
Jan 15, 2020·Pharmaceutical Medicine·Samia A KhanNabih A Baeshen
Aug 12, 2020·Scientific Reports·Barbi GogoiS P Saikia

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Datasets Mentioned

BETA
HQ112416.1
HQ112416

Software Mentioned

BLAST
Perl Catalyst Framework
QRforDNA
Apache
custom Perl scripts
Internet Explorer
QR
Excel
IdentifybyBlast
JAVA

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