EEfinder

EEfinder identifies and classifies bacterial and viral endogenized elements in eukaryotic genomes.

Key Features:

• Data cleaning: Prepares input sequences for downstream analysis.
• Similarity search through sequence alignment: Identifies candidate endogenized elements by aligning sequences against reference databases.
• Filtering candidate elements: Removes spurious hits to retain high-confidence candidates.
• Taxonomy assignment: Assigns taxonomic classification to identified elements.
• Merging of truncated elements: Reconstructs fragmented endogenized elements from multiple adjacent hits.
• Flanks extraction: Retrieves genomic regions adjacent to integrated elements.
• Sensitivity validation: Detected 97% of endogenous viral elements compared to manual curation and identified an almost exact full integration of a Wolbachia genome described by wet-lab experiments.

Scientific Applications:

• Host-pathogen interaction history: Characterizes past interactions and coevolution between hosts and bacteria or viruses through identification of endogenized elements.
• Metagenomic contamination control: Provides reference information to remove false positive results from metagenomic studies.
• Comparative genomics: Facilitates reproducible comparative analysis of endogenized elements across different studies and eukaryotic genomes.

Methodology:

EEfinder implements six steps: data cleaning, similarity search through sequence alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements, and flanks extraction.