DNA Barcode Goes Two-Dimensions: DNA QR Code Web Server

被引：30

作者：

Liu, Chang ^{[1
]}

Shi, Linchun ^{[1
]}

Xu, Xiaolan ^{[1
]}

Li, Huan

Xing, Hang ^{[2
]}

Liang, Dong ^{[2
]}

Jiang, Kun ^{[3
]}

Pang, Xiaohui ^{[1
]}

Song, Jingyuan ^{[1
]}

Chen, Shilin ^{[1
]}

机构：

[1] Chinese Acad Med Sci, Peking Union Med Coll, Inst Med Plant Dev, Beijing 100730, Peoples R China

[2] Beijing Univ Aeronaut, Sch Comp Sci & Engn, Beijing, Peoples R China

[3] Pidit Inc, Edison, NJ USA

来源：

PLOS ONE | 2012年 / 7卷 / 05期

关键词：

GENOMIC SEQUENCE; ALGORITHMS; SPACER;

D O I：

10.1371/journal.pone.0035146

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

引用

页数：7

共 23 条

[1]

Awano T, 2009, P NATL ACAD SCI USA, V106, P2794, DOI [10.1073/pnas.0812297106, 10.1073/pnas.0905845106]

[2] Data structures and compression algorithms for genomic sequence data [J].

Brandon, Marty C. ;

Wallace, Douglas C. ;

Baldi, Pierre .

BIOINFORMATICS, 2009, 25 (14) :1731-1738

[3] A proposal for a standardised protocol to barcode all land plants [J].

Chase, Mark W. ;

Cowan, Robyn S. ;

Hollingsworth, Peter M. ;

van den Berg, Cassio ;

Madrinan, Santiago ;

Petersen, Gitte ;

Seberg, Ole ;

Jorgsensen, Tina ;

Cameron, Kenneth M. ;

Carine, Mark ;

Pedersen, Niklas ;

Hedderson, Terry A. J. ;

Conrad, Ferozah ;

Salazar, Gerardo A. ;

Richardson, James E. ;

Hollingsworth, Michelle L. ;

Barraclough, Timothy G. ;

Kelly, Laura ;

Wilkinson, Mike .

TAXON, 2007, 56 (02) :295-299

[4]

Chen SL, 2010, PLOS ONE, V5, DOI [10.1371/journal.pone.0008613, 10.1371/journal.pone.0015633]

[5] DNACompress: fast and effective DNA sequence compression [J].

Chen, X ;

Li, M ;

Ma, B ;

Tromp, J .

BIOINFORMATICS, 2002, 18 (12) :1696-1698

[6]

ELIAS P, 1975, IEEE T INFORM THEORY, V21, P194, DOI 10.1109/TIT.1975.1055349

[7] Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well [J].

Fazekas, Aron J. ;

Burgess, Kevin S. ;

Kesanakurti, Prasad R. ;

Graham, Sean W. ;

Newmaster, Steven G. ;

Husband, Brian C. ;

Percy, Diana M. ;

Hajibabaei, Mehrdad ;

Barrett, Spencer C. H. .

PLOS ONE, 2008, 3 (07)

[8]

Golomb SW, 1965, IEEE T INFORM THEORY, V12, P317

[9] Barcoding animal life:: cytochrome c oxidase subunit 1 divergences among closely related species [J].

Hebert, PDN ;

Ratnasingham, S ;

deWaard, JR .

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2003, 270 :S96-S99

[10] Choosing and Using a Plant DNA Barcode [J].

Hollingsworth, Peter M. ;

Graham, Sean W. ;

Little, Damon P. .

PLOS ONE, 2011, 6 (05)

← 1 2 3 →