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PMID: 23717618 Published · epublish English Journal Article Research Support, N.I.H., Extramural

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

PloS one ·Vol. 8 ·No. 5 ·2013-00-00 ·Pages e64465

Wang Q, Jia P, Zhao Z

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/.

MeSH Terms
Computational Biology/methods Genome Genomics/methods High-Throughput Nucleotide Sequencing Humans Software Virus Integration Viruses
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Wang Qingguo
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.
Jia Peilin
Zhao Zhongming
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Article Info
Journal
PloS one
Abbr.
PLoS One
ISSN
1932-6203
DOI
10.1371/journal.pone.0064465
Published
2013-00-00
Epub
2013-00-24
Pages
e64465
Language
English
Region
United States
NLM ID
101285081
PMCID
PMC3663743
Subset
IM
Grants
NCI NIH HHS · P50 CA095103 · United States
NLM NIH HHS · R01LM011177 · United States
NCI NIH HHS · P30 CA068485 · United States
NLM NIH HHS · R01 LM011177 · United States
NCI NIH HHS · P50CA095103 · United States
NCI NIH HHS · P30CA68485 · United States
External Links
PubMed source DOI: 10.1371/journal.pone.0064465 PMC Full Text View journal details
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