ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 23314323.
- Also identified by DOI 10.1093/bioinformatics/btt011 and PMC identifier 3582262.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Insertional 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. VFS is distributed under GPL version 3 at http://hkbic.cuhk.edu.hk/software/viralfusionseq
Medical subject headings
- Gene Fusion
- RNA
- Software
- Virus Integration