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

Hocum JD, Battrell LR, Maynard R, Adair JE, Beard BC, Rawlings DJ, Kiem HP, Miller DG, Trobridge GD - BMC Bioinformatics (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. jhocum@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.

No MeSH data available.


Related in: MedlinePlus

VISA is scalable with NGS. Several factors affect the amount of processing time required for an input file, including the number of reads that can be mapped to the genome and the number of files being processed in parallel. Each input file was processed 3 times. Standard error bars are shown
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Fig2: VISA is scalable with NGS. Several factors affect the amount of processing time required for an input file, including the number of reads that can be mapped to the genome and the number of files being processed in parallel. Each input file was processed 3 times. Standard error bars are shown

Mentions: VISA processes sequence reads and identifies unique RISs without adding a substantial amount of time after the alignment process (Fig. 1). Memory efficiency is largely accomplished by employing a MySQL database for the initial alignment filtering. This strategy reduces the strain on the server resources while processing large NGS datasets in parallel. Binning the candidate RISs into 10 bp windows and then designating the unique RISs based on the alignment scores is a time efficient method to identify unique RISs. The compromise between time and memory efficiency allows VISA to be scalable with NGS (Fig. 2).Figure 1


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

Hocum JD, Battrell LR, Maynard R, Adair JE, Beard BC, Rawlings DJ, Kiem HP, Miller DG, Trobridge GD - BMC Bioinformatics (2015)

VISA is scalable with NGS. Several factors affect the amount of processing time required for an input file, including the number of reads that can be mapped to the genome and the number of files being processed in parallel. Each input file was processed 3 times. Standard error bars are shown
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4493804&req=5

Fig2: VISA is scalable with NGS. Several factors affect the amount of processing time required for an input file, including the number of reads that can be mapped to the genome and the number of files being processed in parallel. Each input file was processed 3 times. Standard error bars are shown
Mentions: VISA processes sequence reads and identifies unique RISs without adding a substantial amount of time after the alignment process (Fig. 1). Memory efficiency is largely accomplished by employing a MySQL database for the initial alignment filtering. This strategy reduces the strain on the server resources while processing large NGS datasets in parallel. Binning the candidate RISs into 10 bp windows and then designating the unique RISs based on the alignment scores is a time efficient method to identify unique RISs. The compromise between time and memory efficiency allows VISA to be scalable with NGS (Fig. 2).Figure 1

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. jhocum@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.

No MeSH data available.


Related in: MedlinePlus