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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 requires minimal processing time relative to the alignment process. The processing steps are as follows: (1) Identify LTR-chromosome junctions and generate query sequences, (2) align query sequences to the genome using BLAT, (3) retrieve the top 5 alignments for each query sequence and filter out alignments that cannot be aligned to a unique location in the genome, (4) identify the unique RISs, (5) determine proximity of unique RISs to nearby genes, and (6) prepare the excel and CSV output files. Sequence reads containing lentiviral LTR-chromosome junctions were processed with VISA. 3 input files were used with a mean of 502,083 sequence reads per file. Standard error bars are shown. * indicates the value is less than 1 %
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Fig1: VISA requires minimal processing time relative to the alignment process. The processing steps are as follows: (1) Identify LTR-chromosome junctions and generate query sequences, (2) align query sequences to the genome using BLAT, (3) retrieve the top 5 alignments for each query sequence and filter out alignments that cannot be aligned to a unique location in the genome, (4) identify the unique RISs, (5) determine proximity of unique RISs to nearby genes, and (6) prepare the excel and CSV output files. Sequence reads containing lentiviral LTR-chromosome junctions were processed with VISA. 3 input files were used with a mean of 502,083 sequence reads per file. Standard error bars are shown. * indicates the value is less than 1 %

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 requires minimal processing time relative to the alignment process. The processing steps are as follows: (1) Identify LTR-chromosome junctions and generate query sequences, (2) align query sequences to the genome using BLAT, (3) retrieve the top 5 alignments for each query sequence and filter out alignments that cannot be aligned to a unique location in the genome, (4) identify the unique RISs, (5) determine proximity of unique RISs to nearby genes, and (6) prepare the excel and CSV output files. Sequence reads containing lentiviral LTR-chromosome junctions were processed with VISA. 3 input files were used with a mean of 502,083 sequence reads per file. Standard error bars are shown. * indicates the value is less than 1 %
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: VISA requires minimal processing time relative to the alignment process. The processing steps are as follows: (1) Identify LTR-chromosome junctions and generate query sequences, (2) align query sequences to the genome using BLAT, (3) retrieve the top 5 alignments for each query sequence and filter out alignments that cannot be aligned to a unique location in the genome, (4) identify the unique RISs, (5) determine proximity of unique RISs to nearby genes, and (6) prepare the excel and CSV output files. Sequence reads containing lentiviral LTR-chromosome junctions were processed with VISA. 3 input files were used with a mean of 502,083 sequence reads per file. Standard error bars are shown. * indicates the value is less than 1 %
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