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Identifying viral integration sites using SeqMap 2.0.

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

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Identifying viral integration sites using SeqMap 2.0.

Hawkins Troy B TB Dantzer Jessica J Peters Brandon B Dinauer Mary M Mockaitis Keithanne K Mooney Sean S Cornetta Kenneth K

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]

PMID: 21245052

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