ABSTRACT
DNA barcode sequence is a short DNA sequence representing a sample from a particular species. The commonly used DNA barcodes are at least 200 bps long. This large number of characters cannot be encoded in two-dimensional codes for sample recognition and tracking. In the present study, we described a method that can be used to compress the DNA sequences and then generate the corresponding QR code. With the large numbers of software and hardware, the QR code can be used efficiently for printing, labeling, and scanning.
Subject(s)
DNA Barcoding, Taxonomic , Software , DNA Barcoding, Taxonomic/methods , DNA/genetics , Sequence Analysis, DNA/methodsABSTRACT
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.
Subject(s)
DNA Barcoding, Taxonomic , Data Compression , Animals , DNA, Plant/genetics , Plants/genetics , Algorithms , Sequence Analysis, DNA , PhylogenyABSTRACT
Impetigo herpetiformis is a rare variant of generalized pustular psoriasis that occurs during pregnancy or is triggered by pregnancy, often in association with hypocalcemia. This condition is associated with increased maternal and fetal morbidity and mortality. We report a 29-year-old pregnant woman who presented to hospital at the gestational age of 20 weeks with widespread erythema covered with pustules that coalesced to form lakes of pus. She did not respond to corticosteroids, immunosuppressants, or phototherapy. Finally, intra-amniotic injection of ethacridine lactate was administered to terminate the pregnancy, and the patient showed complete recovery in 3 months. Insight from this case report may facilitate optimal management of this relatively rare entity.
