Vgas: A Viral Genome Annotation System

作者：Kai-Yue Zhang, Yi‐Zhou Gao, Meng‐Ze Du, Shuo Liu, Chuan Dong, Feng‐Biao Guo · 发表于：Frontiers in Microbiology · 年份：2019 · DOI：10.3389/fmicb.2019.00184 · 被引用次数：59 · 研究领域：Genomics and Phylogenetic Studies、Bacteriophages and microbial interactions、RNA and protein synthesis mechanisms

The in-depth study of viral genomes is of great help in many aspects, especially in the treatment of human diseases caused by viral infections. With the rapid accumulation of viral sequencing data, improved or alternative gene-finding systems have become necessary to process and mine these data. In this article, we present Vgas, a system combining an ab initio method and a similarity-based method to automatically find viral genes and perform gene function annotation. Vgas has compared with existing programs, such as Prodigal, GeneMarkS and Glimmer. Through testing 5705 virus genomes downloaded from RefSeq, Vgas demonstrated its superiority with the highest average precision and recall (both indexes were 1% higher or more than the other programs); particularly for small virus genomes (≤10 kb), it showed significantly improved performance (precision was 6% higher, and recall was 2% higher). Moreover, Vgas presents an annotation module to provide functional information for predicted genes based on BLASTp alignment. This characteristic may be specifically useful in some cases. When combining Vgas with GeneMarkS and Prodigal, better prediction results could be obtained than with each of the three individual programs, suggesting that collaborative prediction using several different software programs will be an alternative for gene predicting. Vgas is freely available at http://cefg.uestc.cn/vgas/ or http://121.48.162.133/vgas/. We hope that Vgas could be an alternative virus gene f...