ALIENNESS

ALIENNESS detects candidate horizontal gene transfers by parsing BLAST results against public protein libraries (NCBI) and computing an Alien Index that compares best BLAST E-values between donor and recipient taxa.

Key Features:

• Taxonomy-Aware Analysis: Allows definition of recipient (e.g., Metazoa) and donor (e.g., bacteria, fungi) branches using the NCBI taxonomy to focus HGT detection on specified evolutionary lineages.
• Integration with BLAST Results: Processes BLAST output of a proteome derived from searches against public protein libraries available through the National Center for Biotechnology Information (NCBI).
• Alien Index Calculation: Computes an Alien Index per query protein by comparing best-hit BLAST E-values between candidate donor and recipient taxa, where AI>0 indicates a stronger alignment to donor taxa and higher AI reflects larger E-value disparity.
• Rapid and Comprehensive Scanning: Scans entire proteomes to identify and rank candidate HGT events across diverse taxa.

Scientific Applications:

• Exploration of Evolutionary Mechanisms: Identification of candidate HGT events to study the role of gene transfer in adaptation and speciation.
• Research on Non-Metazoan Organisms: Detection validated against phylogenetically confirmed HGTs, including plant-parasitic nematodes, to study genetic evolution in non-metazoan taxa.
• Facilitation of Genomic Studies: Enables comparative genomic analyses across a wide range of taxa by flagging proteins with donor-like sequence similarity profiles.

Methodology:

ALIENNESS parses BLAST results against public protein libraries, accepts proteome BLAST outputs with user-specified recipient and donor branches in the NCBI taxonomy, and calculates an Alien Index for each protein based on best-hit E-value comparisons.