VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue.
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- Record sourced from PubMed, PMID 23162058.
- Also identified by DOI 10.1093/bioinformatics/bts665 and PMC identifier 3546792.
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Abstract
We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on whole-transcriptome sequencing (RNA-Seq) data of 256 human cancer samples from The Cancer Genome Atlas. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole-genome sequencing data of human tissue. VirusSeq has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/∼xsu1/VirusSeq.html. xsu1@mdanderson.org Supplementary data are available at Bioinformatics online.
Medical subject headings
- Neoplasms
- Software
- Virus Integration
- Viruses