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May 10, 2025;23 (1):

VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences.

Tao Zhang 张韬, Yiyun Liu 刘依云, Xutong Guo 郭栩彤, Xinran Zhang 张欣然, Xinchang Zheng 郑欣畅, Mochen Zhang 张陌尘, Yiming Bao 鲍一明
Author Information
  1. Tao Zhang 张韬: National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China. ORCID
  2. Yiyun Liu 刘依云: National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China. ORCID
  3. Xutong Guo 郭栩彤: National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China. ORCID
  4. Xinran Zhang 张欣然: National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China. ORCID
  5. Xinchang Zheng 郑欣畅: National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China. ORCID
  6. Mochen Zhang 张陌尘: National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China. ORCID
  7. Yiming Bao 鲍一明: National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China. ORCID
PMID: 39540753 DOI: 10.1093/gpbjnl/qzae082

Abstract

The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable, universal, and automated preliminary taxonomic framework for comprehensive virus studies. Here, we introduce Virus Sequence-based Taxonomy Assignment (VISTA), a computational tool that employs a novel pairwise sequence comparison system and an automatic demarcation threshold identification framework for virus taxonomy. Leveraging physio-chemical property sequences, k-mer profiles, and machine learning techniques, VISTA constructs a robust distance-based framework for taxonomic assignment. Functionally similar to Pairwise Sequence Comparison (PASC), a widely used virus assignment tool based on pairwise sequence comparison, VISTA demonstrates superior performance by providing significantly improved separation for taxonomic groups, more objective taxonomic demarcation thresholds, greatly enhanced speed, and a wider application scope. We successfully applied VISTA to 38 virus families, as well as to the class Caudoviricetes. This demonstrates VISTA's scalability, robustness, and ability to automatically and accurately assign taxonomy to both prokaryotic and eukaryotic viruses. Furthermore, the application of VISTA to 679 unclassified prokaryotic virus genomes recovered from metagenomic data identified 46 novel virus families. VISTA is available as both a command line tool and a user-friendly web portal at https://ngdc.cncb.ac.cn/vista.

Keywords

Demarcation Pairwise sequence comparison Unclassified virus Viral genome Virus taxonomic assignment

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MeSH Term

Genome, Viral
Software
Viruses
Phylogeny
Computational Biology
Journal Article

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