Eagle

Eagle identifies pathogen-specific genomic signatures using an alignment-free analysis of relative absent words (RAW) in genomic sequences for comparative detection against a reference genome.

Key Features:

• Alignment-Free Methodology: Bypasses sequence alignment by analyzing presence/absence patterns of short DNA sequences across genomes.
• Relative Absent Words (RAW): Calculates RAWs to detect short sequences that are absent in a reference genome but present in target pathogen genomes.
• Reference-Based Comparative Analysis: Employs a reference sequence (e.g., the human genome) for comparative identification of pathogen-specific absent/present words.

Scientific Applications:

• Infectious disease research: Identifies pathogen-specific genomic signatures for surveillance and outbreak analysis.
• Ebola virus case study: Detected 12–14 nucleotide sequences that were present in all Ebola virus genomes but absent from the human genome and located consistently on two Ebola virus proteins across strains.
• Diagnostic and therapeutic target discovery: Highlights conserved pathogen sequences that can serve as candidates for diagnostic markers or therapeutic intervention points.

Methodology:

Computes relative absent words by scanning genomic sequences to detect short DNA segments absent from a reference genome (e.g., human) but present in pathogen genomes, using an alignment-free comparative analysis.