OrthoAlign

OrthoAlign aligns orthologous genes across genomes to solve the gene order alignment problem by accounting for genome-wide evolutionary events such as duplications, losses, rearrangements, and substitutions to study genomic evolution.

Key Features:

• Gene order alignment: Aligns orthologous genes across species to address the gene order alignment problem.
• Evolutionary event modeling: Explicitly accounts for duplications, losses, rearrangements, inversions, and substitutions within its algorithm.
• Phylogenetic integration: Operates in a phylogenetic context to infer evolutionary histories of gene repertoires.
• Event characterization: Analyzes event type, genomic location, distribution, and length for detected evolutionary events.
• Ancestral reconstruction: Infers ancestral configurations of gene order and gene repertoires.
• Quantitative rate estimation: Estimates rates of duplications, losses, and inversions and enables quantitative comparisons between taxa.
• Empirical application: Applied to tRNA repertoires across 50 fully sequenced Bacillus genomes for empirical inference.

Scientific Applications:

• Phylogenetic inference of gene repertoires: Infers evolutionary histories of gene repertoires within a phylogenetic framework.
• tRNA repertoire analysis: Analyzes transfer RNA (tRNA) repertoires across 50 Bacillus genomes, revealing a predominance of gene duplications and losses over rearrangement events.
• Comparative genomics: Quantifies and compares event rates between taxa, for example finding duplications 24 times less frequent and losses and inversions 12 times lower in Bacillus than in Escherichia coli.
• Detection of selective pressures: Identifies signatures of selective pressure on gene repertoires, such as constraints on tRNA gene evolution via rate and distribution analyses.

Methodology:

Aligns orthologous genes while integrating duplications, losses, rearrangements, inversions, and substitutions within a phylogenetic context, characterizing event type, location, distribution, and length and inferring ancestral configurations.