Vgas: A Viral Genome Annotation System

Frontiers in Microbiology
Kai-Yue ZhangFeng-Biao Guo

Abstract

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 was compared with existing programs, such as Prodigal, GeneMarkS, and Glimmer. Through testing 5,705 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 ...Continue Reading

References

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Citations

May 26, 2020·BMC Bioinformatics·Alejandro A SchäfferEric P Nawrocki
Aug 29, 2020·Virology Journal·Christian Jean MichelJulie Dawn Thompson
Jul 6, 2020·Computational Biology and Chemistry·Alicia Jiménez-AlbertoJuan A Castelán-Vega
Feb 5, 2021·Briefings in Bioinformatics·Yibo DongXiaoming Liu
Feb 9, 2021·Mitochondrial DNA. Part B, Resources·Ting LvYanming Fang
Oct 24, 2020·Microbiology Resource Announcements·Elisabeth MathijsKris De Clercq
Aug 19, 2021·PLoS Pathogens·Tarcísio Fontenele de BritoAttilio Pane
Aug 27, 2021·Microbiology Resource Announcements·Naazneen MoollaJacqueline Weyer
Dec 17, 2021·PLoS Computational Biology·Jordan J BakerJulia Schaletzky

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Software Mentioned

GS
ZCUVE
GeneMarkS
ZCURVE
Glimmer3
Glimmer
finder
GeneMark
Prodigal
Vgas

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