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Gigascience. 2018 Jan 1;7(1):1-7. doi: 10.1093/gigascience/gix123.

BS-virus-finder: virus integration calling using bisulfite sequencing data.

Gao S1,2,3,4,5,6, Hu X2,3, Xu F3,7,8, Gao C9, Xiong K10, Zhao X2,11, Chen H3,8, Zhao S3,4, Wang M3, Fu D2, Zhao X12, Bai J3, Mao L3, Li B2,3, Wu S5, Wang J3, Li S2,13,14, Yang H3,4,11, Bolund L6, Pedersen CNS1.

Author information

1
Bioinformatics Research Center, Aarhus University, C. F. Møllers Allé 8, DK-8000, Aarhus C, Denmark.
2
Forensics Genomics International (FGI), BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.
3
BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.
4
James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
5
The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China.
6
Department of Biomedicine, Aarhus University, Vennelyst Boulevard 4, DK-8000 Aarhus C, Denmark.
7
Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
8
China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.
9
College of Computer Science and Technology, Qingdao University, Qingdao 266071, China.
10
Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, DK-1870 Frederiksberg C, Denmark.
11
BGI Education Center, University of Chinese Academy of Sciences, Beijing 100049, China.
12
College of Mathematics & Statistics, Changsha University of Science and Technology, Changsha 410114, China.
13
Shenzhen Key Laboratory of Forensics, BGI-Shenzhen, Shenzhen 518083, China.
14
College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an 710049, China.

Abstract

Background:

DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data.

Findings:

We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF.

Conclusions:

BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.

KEYWORDS:

bisulfite sequencing; carcinogenesis; virus integration

PMID:
29267855
PMCID:
PMC5788064
DOI:
10.1093/gigascience/gix123
[Indexed for MEDLINE]
Free PMC Article

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