Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 May 24;8(5):e64465.
doi: 10.1371/journal.pone.0064465. Print 2013.

VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data

Qingguo Wang  1 , Peilin Jia, Zhongming Zhao
Affiliations

VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data

Qingguo Wang et al. PLoS One. .

Abstract

Next generation sequencing (NGS) technologies allow us to explore virus interactions with host genomes that lead to carcinogenesis or other diseases; however, this effort is largely hindered by the dearth of efficient computational tools. Here, we present a new tool, VirusFinder, for the identification of viruses and their integration sites in host genomes using NGS data, including whole transcriptome sequencing (RNA-Seq), whole genome sequencing (WGS), and targeted sequencing data. VirusFinder's unique features include the characterization of insertion loci of virus of arbitrary type in the host genome and high accuracy and computational efficiency as a result of its well-designed pipeline. The source code as well as additional data of VirusFinder is publicly available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.

PubMed Disclaimer

Conflict of interest statement

Competing Interests: The authors have the following interest. Zhongming Zhao has served as an editorial board member of PLOS ONE since 2010. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. VirusFinder’s pipeline to detect viruses and their integration sites in next generation sequencing (NGS) data.
VirusFinder overall follows a three-step procedure: (1) preprocessing, (2) virus detection, and (3) virus integration site detection. The current version of VirusFinder (release 1.0) uses UCSC hg19 (http://hgdownload.cse.ucsc.edu/downloads.html#human) as reference human genome. DB: database. SVs: structural variants (especially inter-chromosomal translocations).
See this image and copyright information in PMC

References

    1. Lace MJ, Anson JR, Klussmann JP, Wang DH, Smith EM, et al. (2011) Human papillomavirus type 16 (HPV-16) genomes integrated in head and neck cancers and in HPV-16-immortalized human keratinocyte clones express chimeric virus-cell mRNAs similar to those found in cervical cancers. J Virol 85: 1645–1654. - PMC - PubMed
    1. Sung W-K, Zheng H, Li S, Chen R, Liu X, et al. (2012) Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet 44: 765–769. - PubMed
    1. Jiang Z, Jhunjhunwala S, Liu J, Haverty PM, Kennemer MI, et al. (2012) The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res 22: 593–601. - PMC - PubMed
    1. Lasithiotaki I, Antoniou K m., Derdas S p., Sarchianaki E, Symvoulakis E k., et al... (2013) The presence of Merkel cell polyomavirus is associated with deregulated expression of BRAF and Bcl-2 genes in non-small cell lung cancer. International Journal of Cancer. Doi: 10.1002/ijc.28062. - PubMed
    1. Ding D, Lou X, Hua D, Yu W, Li L, et al. (2012) Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing-based approach. PLoS Genet 8: e1003065. - PMC - PubMed

Publication types