LV Barcoding: locality sensitive hashing-based tool for rapid species identification in DNA barcoding

摘要

DNA barcoding has emerged as a cost-effective approach for speciesidentification. However, the scarcity of tools used for searching the boomingreference database becomes an obstacle, currently with BLAST as the onlypractical choice. Here, we propose a program - LV Barcoding - based on both therandom hyperplane projection-based locality sensitive hashing method and thecomposition vector-based VIP Barcoding for fast species identification. Theperformance of LV Barcoding is assessed on the data release of BOLD. LVBarcoding has higher accuracy than BLAST, and is able to match a single queryagainst ~114,000 reference barcodes within 10 seconds on a desktop computer.This program is available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.