VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.
BMC Bioinformatics
; 16: 212, 2015 Jul 07.
Article
en En
| MEDLINE
| ID: mdl-26150117
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.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Retroviridae
/
Programas Informáticos
/
Genoma Humano
/
Integración Viral
/
Internet
/
Secuenciación de Nucleótidos de Alto Rendimiento
/
Vectores Genéticos
Tipo de estudio:
Prognostic_studies
Límite:
Humans
Idioma:
En
Revista:
BMC Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2015
Tipo del documento:
Article
País de afiliación:
Estados Unidos