Dataset Information
Identifying viral integration sites using SeqMap 2.0.
Ontology highlight
ABSTRACT: Unlabelled
Retroviral integration has been implicated in several biomedical applications, including identification of cancer-associated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration.Availability and implementation
The method is implemented in a publicly accessible web server platform, SeqMap 2.0, containing analysis tools and both private and shared lab workspaces that facilitate collaboration among researchers. Available at http://seqmap.compbio.iupui.edu/.
SUBMITTER: Hawkins TB
PROVIDER: S-EPMC3042184 | biostudies-literature | 2011 Mar
REPOSITORIES: biostudies-literature
Publications
Identifying viral integration sites using SeqMap 2.0.
Bioinformatics (Oxford, England) 20110117 5
<h4>Unlabelled</h4>Retroviral integration has been implicated in several biomedical applications, including identification of cancer-associated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used ...[more]
