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VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing
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 dev...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493804/ https://www.ncbi.nlm.nih.gov/pubmed/26150117 http://dx.doi.org/10.1186/s12859-015-0653-6 |
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author | Hocum, Jonah D. Battrell, Logan R. Maynard, Ryan Adair, Jennifer E. Beard, Brian C. Rawlings, David J. Kiem, Hans-Peter Miller, Daniel G. Trobridge, Grant D. |
author_facet | Hocum, Jonah D. Battrell, Logan R. Maynard, Ryan Adair, Jennifer E. Beard, Brian C. Rawlings, David J. Kiem, Hans-Peter Miller, Daniel G. Trobridge, Grant D. |
author_sort | Hocum, Jonah D. |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0653-6) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4493804 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-44938042015-07-08 VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing Hocum, Jonah D. Battrell, Logan R. Maynard, Ryan Adair, Jennifer E. Beard, Brian C. Rawlings, David J. Kiem, Hans-Peter Miller, Daniel G. Trobridge, Grant D. BMC Bioinformatics Software 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0653-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-07-07 /pmc/articles/PMC4493804/ /pubmed/26150117 http://dx.doi.org/10.1186/s12859-015-0653-6 Text en © Hocum et al. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Hocum, Jonah D. Battrell, Logan R. Maynard, Ryan Adair, Jennifer E. Beard, Brian C. Rawlings, David J. Kiem, Hans-Peter Miller, Daniel G. Trobridge, Grant D. VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing |
title | VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing |
title_full | VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing |
title_fullStr | VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing |
title_full_unstemmed | VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing |
title_short | VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing |
title_sort | visa - vector integration site analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493804/ https://www.ncbi.nlm.nih.gov/pubmed/26150117 http://dx.doi.org/10.1186/s12859-015-0653-6 |
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