title: Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource.
abstract: Research in gene therapy involving genome-integrating vectors now often includes analysis of vector integration sites across the genome using methods such as ligation-mediated PCR (LM-PCR) or linear amplification-mediated PCR (LAM-PCR). To help researchers analyze these sites and the functions of nearby genes, we have developed SeqMap (http://seqmap.compbio.iupui.edu/) a secure, web-based comprehensive vector integration site management tool that automatically analyzes and annotates large numbers of vector integration sites derived from LM-PCR experiments in human and model organisms upon a common genome database. We believe the use of this resource will enable better reproducibility and understanding of this important data.
authors.affiliation: Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA.
authors.forename: B
authors.initials: B
authors.lastname: Peters
authors.forename: S
authors.initials: S
authors.lastname: Dirscherl
authors.forename: J
authors.initials: J
authors.lastname: Dantzer
authors.forename: J
authors.initials: J
authors.lastname: Nowacki
authors.forename: S
authors.initials: S
authors.lastname: Cross
authors.forename: X
authors.initials: X
authors.lastname: Li
authors.forename: K
authors.initials: K
authors.lastname: Cornetta
authors.forename: M C
authors.initials: MC
authors.lastname: Dinauer
authors.forename: S D
authors.initials: SD
authors.lastname: Mooney
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D030541:Databases, Genetic; D015316:Genetic Therapy; D016678:Genome; D006801:Humans; D019426:Integrases / Q000235:genetics*; D020407:Internet; D016133:Polymerase Chain Reaction / Q000379:methods; D012106:Research; D012190:Retroviridae / Q000235:genetics; D012984:Software; D016662:Virus Integration / Q000235:genetics*
chemical_list: D019426:Integrases