OrtholugeDB

OrthoLugeDB predicts orthologs across completely sequenced bacterial and archaeal genomes to distinguish orthologs from paralogs and support functional annotation in comparative genomics.

Key Features:

• Taxonomic scope: Operates on completely sequenced bacterial and archaeal genomes.
• Ortholog versus paralog discrimination: Distinguishes orthologs (speciation-derived) from paralogs (duplication-derived) to improve inference of gene function conservation.
• Reciprocal best BLAST hits: Generates initial ortholog predictions using reciprocal best hits from the Basic Local Alignment Search Tool (BLAST).
• OrthoLuge refinement: Refines ortholog assignments using the OrthoLuge method based on phylogenetic distance ratios.
• Single-gene and genome-wide analysis: Supports analyses at the level of individual genes and entire genomes.
• Cross-taxonomic performance: Designed to identify orthologs consistently across a wide range of taxonomic distances for large-scale predictions.
• Functional annotation support: Facilitates transfer and improvement of functional annotations in microbial genomes through robust ortholog identification.

Scientific Applications:

• Comparative genomics: Identification of orthologous genes for cross-species genomic comparisons in bacteria and archaea.
• Functional annotation transfer: Propagation and refinement of gene function annotations based on orthology relationships.
• Large-scale ortholog prediction: Generation of ortholog sets across many genomes to support pan-genome and evolutionary studies.
• Gene evolutionary inference: Resolving gene histories by distinguishing speciation-derived orthologs from duplication-derived paralogs.

Methodology:

OrthoLugeDB derives ortholog predictions from reciprocal best BLAST hits and refines them with the OrthoLuge method using phylogenetic distance ratios.