ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution
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AbstractInsertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and expressed viral fusion events are still limited. Here, we present ViralFusionSeq (VFS), which combines soft-clipping information, read-pair analysis and targeted de novo assembly to discover and annotate viral-human fusions. VFS was used in an RNA-Seq experiment, simulated DNA-Seq experiment and re-analysis of published DNA-Seq datasets. Our experiments demonstrated that VFS is both sensitive and highly accurate.
All Author(s) ListLi JW, Wan R, Yu CS, Co NN, Wong N, Chan TF
Journal nameBioinformatics
Year2013
Month3
Day1
Volume Number29
Issue Number5
PublisherOXFORD UNIV PRESS
Pages649 - 651
ISSN1367-4803
eISSN1460-2059
LanguagesEnglish-United Kingdom
Web of Science Subject CategoriesBiochemical Research Methods; BIOCHEMICAL RESEARCH METHODS; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; BIOTECHNOLOGY & APPLIED MICROBIOLOGY; Computer Science; Computer Science, Interdisciplinary Applications; Mathematical & Computational Biology; MATHEMATICAL & COMPUTATIONAL BIOLOGY; Mathematics; Statistics & Probability

Last updated on 2021-20-09 at 23:59