qMGR

qMGR: Quantitative analysis of mitochondrial genome rearrangements

qMGR quantifies mitochondrial genome (mitogenome) rearrangements by treating each gene as an individual structural unit and calculating rearrangement frequency (RF) and rearrangement score (RS) relative to a selected reference arrangement.

Key Features:

• Gene-level rearrangement metrics: Calculates RF and RS for individual genes by accumulating changes between the two nearest neighbor genes compared to a typical vertebrate or invertebrate reference arrangement.
• Genome-level scoring: Aggregates gene-level RS values to derive an overall mitogenome rearrangement score for each genome.
• Conserved and variable segment identification: Detects conserved gene sets and genomic segments with high rearrangement frequency within taxonomic groups.

Scientific Applications:

• Mitogenome evolution analysis: Quantifies rearrangement patterns to assess evolutionary distances, infer mechanisms of mitochondrial genome rearrangement, and enable standardized large-scale comparative analyses across taxa.

Methodology:

Users select a reference gene arrangement (typical vertebrate or invertebrate) and input one or more mitogenome arrangements from the target taxon. qMGR compares each genome to the reference, accumulates nearest-neighbor gene changes to compute gene-level RS and RF, and sums RS values to generate a comprehensive rearrangement score for each mitogenome.