title: VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  VirusSeq has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/∼xsu1/VirusSeq.html.
  
  
  BACKGROUND
  xsu1@mdanderson.org
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
authors.forename: Yunxin
authors.initials: Y
authors.lastname: Chen
authors.forename: Hui
authors.initials: H
authors.lastname: Yao
authors.forename: Erika J
authors.initials: EJ
authors.lastname: Thompson
authors.forename: Nizar M
authors.initials: NM
authors.lastname: Tannir
authors.forename: John N
authors.initials: JN
authors.lastname: Weinstein
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Su
mesh_terms: D000465:Algorithms; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009369:Neoplasms / Q000235:genetics / Q000821:virology*; D017423:Sequence Analysis, RNA; D012984:Software; D016662:Virus Integration; D014780:Viruses / Q000235:genetics / Q000302:isolation & purification*