detectEVE

detectEVE identifies non-retroviral endogenous viral elements (nrEVEs) in genomic assemblies using a confidence-scoring system for protein sequence similarity searches.

Key Features:

• Confidence scoring system: Assigns confidence scores to hits in protein sequence similarity searches using bit score distributions and search hints related to various viral characteristics.
• Computational efficiency: Executes with resource-efficient parallel execution, making it considerably faster than existing approaches.
• Workflow implementation: Implemented as a snakemake workflow for reproducible and scalable analysis.

Scientific Applications:

• Genome annotation enhancement: Enhances genome annotations with metadata for EVE loci.
• Paleo-virological studies: Conducts large-scale paleo-virological studies to explore deep viral evolutionary histories.
• Transcriptomic analysis: Aids in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.

Methodology:

detectEVE performs protein sequence similarity searches and implements a scaling system that assigns confidence scores to hits using bit score distributions and search hints related to various viral characteristics.