VirusSeq

VirusSeq detects known viral sequences and maps their integration sites in human genomes from next-generation sequencing (NGS) data to enable analysis of viral involvement in human disease, including cancer.

Key Features:

• Detection Capability: Identifies known viral sequences within human NGS data with reported high sensitivity and specificity.
• Integration Site Mapping: Pinpoints viral integration sites within the human genome to assess potential impacts on gene function and oncogenesis.
• Data Compatibility and Validation: Operates on whole-transcriptome sequencing (RNA-Seq) and whole-genome sequencing data and was validated on 256 human cancer samples from The Cancer Genome Atlas (TCGA).
• Implementation: Implemented in PERL.

Scientific Applications:

• Cancer Research: Enables identification of viral integrations to investigate roles in oncogenesis and to support discovery of potential therapeutic targets or diagnostic markers.
• Viral–Host Interaction Studies: Applicable to studies of viral-host interactions across human tissues beyond oncology.

Methodology:

Analyzes RNA-Seq and whole-genome sequencing data using algorithmic techniques to detect viral sequences and identify integration sites; validated on 256 TCGA whole-transcriptome samples.