DDQR (dynamic DNA QR coding): An efficient algorithm to represent DNA barcode sequences

• Published in: PloS one Vol. 18; no. 1; p. e0279994
• Main Authors: Wang, Yujun, Yao, Xinjing, Liu, Rui, Liu, Chang
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.01.2023; Public Library of Science (PLoS)
• Subjects: Algorithms; Animals; Bar codes; Binary codes; Binary digits; Biological materials; Biology and life sciences; Compression; Computer and information sciences; Data Compression; Decoding; Deoxyribonucleic acid; DNA; DNA barcoding; DNA Barcoding, Taxonomic; DNA, Plant - genetics; Engineering and Technology; Food industry; Gene sequencing; Genomes; Huffman codes; Medicine and Health Sciences; Methods; Nucleotide sequence; Phylogeny; Physical Sciences; Plants - genetics; Representations; Research and analysis methods; Sequence Analysis, DNA; Taxonomy; Traditional medicine; Upgrading; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0279994

A DNA barcode is a short piece of standard DNA sequence used for species determination and discrimination. Representation of DNA barcodes is essential for DNA barcodes’ applications in the transportation and recognition of biological materials. Previously, we have compared different strategies for representing the DNA barcodes. In the present study, we have developed a compression algorithm based on binary coding or Huffman coding scheme, followed by converting the binary digits into Base64 digits. The combination of this compression algorithm and the QR representation leads to the dynamic DNA QR coding algorithm (DDQR). We tested the DDQR algorithm on simulated data and real DNA barcode sequences from the commonly used plant and animal DNA barcode markers: rbcL, matK, trnH-psbA, ITS2, and COI. We compared the compression efficiency of DDQR and another state-of-the-art DNA compression algorithm GeCo3 for sequences with various base compositions and lengths. We found that DDQR had a higher compression rate than GeCo3 for DNA sequences shorter than 800 bp, which is the typical size range for DNA barcodes. We also upgraded a web server ( http://www.1kmpg.cn/ddqr ) that provides three functions: retrieval of DNA barcode sequences, encoding DNA barcode sequences to DDQR codes, and decoding DDQR codes to DNA barcode sequences. The DDQR algorithm and the webserver will be invaluable to applying DNA barcode technology in the food and traditional medicine industries.