fDOG

fDOG traces ortholog distributions across large taxon sets using profile-based searches that score protein feature architecture differences between seed proteins and their orthologs.

Key Features:

• Profile-based ortholog search: Performs ortholog searches starting from a single protein sequence as a seed without requiring comparison of entire proteomes.
• Protein feature architecture scoring: Routinely scores protein feature architecture differences between the seed protein and its orthologs to identify functional modifications.
• Large-scale taxonomic coverage: Enables ortholog searches across more than 18,000 taxa, exceeding the capacity of current state-of-the-art software.
• Presence-absence visualization: Supports visualization of ortholog presence-absence patterns using Uniform Manifold Approximation and Projection to highlight taxa with recent enzyme repertoire changes.

Scientific Applications:

• Plant cell wall-degrading enzyme distribution: Maps the repertoire of plant cell wall-degrading enzymes across the tree of life, including identification of horizontal gene transfer events in invertebrates.
• Evolutionary pattern identification: Reveals evolutionary patterns and functional modifications within genomes through multi-scale analysis from tree of life-wide surveys to individual feature architecture changes.
• Lifestyle change detection: Identifies taxa where recent changes in enzyme repertoires indicate lifestyle changes, such as lineages contributing to the global carbon cycle.

Methodology:

fDOG uses a profile-based approach starting from a single protein sequence as a seed to search for orthologs, with routine scoring of protein feature architecture differences between seed proteins and identified orthologs.