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Identifying viral integration sites using SeqMap 2.0.
Bioinformatics. 2011 Mar 1;27(5):720-2
Authors: Hawkins TB, Dantzer J, Peters B, Dinauer M, Mockaitis K, Mooney S, Cornetta K
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/.
PMID: 21245052 [PubMed - indexed for MEDLINE]
More...
Identifying viral integration sites using SeqMap 2.0.
Bioinformatics. 2011 Mar 1;27(5):720-2
Authors: Hawkins TB, Dantzer J, Peters B, Dinauer M, Mockaitis K, Mooney S, Cornetta K
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/.
PMID: 21245052 [PubMed - indexed for MEDLINE]
More...