iLoci

iLoci parses annotated genome assemblies into interval loci (iLoci) to provide a stable, coordinate-centric framework for computing locus-level statistics and assessing genome organization and annotation changes.

Key Features:

• Alternative Coordinate System: Provides a coordinate system of iLoci that remains stable across assembly and annotation version changes.
• Locus-level Statistical Assessment: Computes statistics on iLoci to quantify genome content, completeness, and annotation accuracy.
• Genome Compactness Measure: Implements a defined metric for relative genome compactness to quantify genome structure.
• Gene Arrangement Analysis: Derives genome-wide characteristics of gene arrangements from iLocus statistics.
• Persistent and Species-specific Statistics: Produces persistent and species-specific genome statistics to accommodate frequent assembly and annotation updates.
• Gene-structure-model-centric Coordinate Storage: Uses a gene-structure-model-centric coordinate system to store and track updates in assemblies or annotations.

Scientific Applications:

• Genome Organization Studies: Enables large-scale, computational detection of species- and clade-specific patterns in genome organization using iLocus analyses.
• Comparative Genomics: Maintains consistent locus coordinates across versions to support comparative analyses of genomes and annotations.
• Genomic Quality Control: Provides locus-level statistics for rigorous quality control of genome assemblies and annotations.

Methodology:

Parses annotated genome assemblies into interval loci; computes locus-level statistics on iLoci; derives a relative genome compactness metric; generates persistent and species-specific statistics; and maps assembly or annotation updates via a gene-structure-model-centric coordinate system.