rearrvisr

rearrvisr identifies and visualizes inter- and intrachromosomal genome rearrangements by projecting translocations and inversions onto a focal genome relative to an ancestral genome reconstruction or another extant genome.

Key Features:

• Implementation: Provided as an R package implementing the described algorithms.
• Identification and classification: Employs a novel algorithm to identify and classify genomic rearrangements, including inter- and intrachromosomal translocations and inversions, projected onto a single focal genome.
• Breakpoints and synteny blocks: Detects breakpoints and synteny blocks along the focal genome and exports results in tabular format.
• Visualization capabilities: Provides two graphical functions to visualize rearrangements and synteny blocks directly along the focal genome.
• Validation metrics: Demonstrates high precision and recall on simulated data.
• Empirical application: Applied to publicly available Drosophila genomes for real-data analyses.

Scientific Applications:

• Evolutionary Biology: Mapping rearrangements onto a focal genome to study the role of structural changes in species divergence and adaptation.
• Genomic Medicine: Characterizing structural variants that may affect gene function or regulation to inform studies of disease-associated genomic alterations.

Methodology:

Detects deviations in gene order between genomes, projects those deviations onto a focal genome, identifies breakpoints and synteny blocks, and classifies events into specific rearrangement types; validated on simulated and real genomic data.