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BMC Bioinformatics. 2015 Jul 7;16:212. doi: 10.1186/s12859-015-0653-6.

VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.

Author information

1
Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. jhocum@wsu.edu.
2
Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. logan_battrell@wsu.edu.
3
Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. ryan.maynard@wsu.edu.
4
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA. jadair@fhcrc.org.
5
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA. bbeard@fhcrc.org.
6
Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA. drawling@uw.edu.
7
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA. hkiem@fhcrc.org.
8
Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA. dgmiller@uw.edu.
9
Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. grant.trobridge@wsu.edu.
10
School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA. grant.trobridge@wsu.edu.

Abstract

BACKGROUND:

Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens.

RESULTS:

We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads.

CONCLUSIONS:

VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.

PMID:
26150117
PMCID:
PMC4493804
DOI:
10.1186/s12859-015-0653-6
[Indexed for MEDLINE]
Free PMC Article

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