Virus Database and Online Inquiry System Based on Natural Vectors

Dong, Rui; Zheng, Hui; Tian, Kun; Yau, Shek-Chung; Mao, Weiguang; Yu, Wenping; Yin, Changchuan; Yu, Chenglong; He, Rong Lucy; Yang, Jie; Yau, Stephen ST

More and more new deadly viruses have been discovered, such as human immunodeficiency virus, severe acute respiratory syndrome, Ebola virus, West Nile virus, H7N9, and their variants. They continually threaten human's life. Nowadays, scientists are able to study the nucleotide sequences of viruses and develop algorithms to classify and predict the characteristics of new viruses. One major approach is to analyze the similarity between the new viruses and known ones. Multiple sequence alignment (MSA) has been widely accepted and used by biologists and virologists now. However, its heavy computational cost causes serious inefficiency, which makes it impossible to analyze the phylogeny of whole genomes. Besides, MSA methods may fail in diverse systems of different families of RNA viruses. Meantime, different evolutionary models can lead to different results, which implies that the models and assumptions are unnatural and unpersuasive. Another popular category of alignment-free methods is based on the statistics of oligomers frequency and associated with a fixed-length segment, known as k-mers. However, it ignores the positional information of nucleotides.