Identifying viral integration sites using SeqMap 2.0.
basic_science · Level V
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- Record sourced from PubMed, PMID 21245052.
- Also identified by DOI 10.1093/bioinformatics/btq722 and PMC identifier 3042184.
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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/.
Medical subject headings
- High-Throughput Nucleotide Sequencing
- Retroviridae
- Software
- Virus Integration