Synima

Synima visualizes synteny and ortholog relationships across annotated genome assemblies to detect and represent evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation.

Key Features:

• Implementation: Implemented in Perl and leveraging R for graphical output.
• Orthologue input: Accepts orthologues derived from reciprocal best BLAST hits, OrthoMCL, or DAGchainer.
• Synteny visualization: Produces genome-wide synteny visualizations across multiple annotated genomes.
• Output format: Exports high-quality figures in PDF format.
• Configurable graphics: Provides graphical parameters (size, colors, order, labels) via a configuration file that is initially generated and can be edited.
• Integration: Integrates with reciprocal best BLAST hits, OrthoMCL, and DAGchainer within its package to support synteny analysis workflows.

Scientific Applications:

• Evolutionary analysis: Visualizing synteny to detect genome expansion, chromosomal rearrangement, and chromosomal translocation.
• Comparative genomics: Comparing genome architecture across multiple annotated assemblies.
• Orthology assessment: Supporting ortholog prediction and validation using inputs from reciprocal best BLAST hits, OrthoMCL, or DAGchainer.
• Figure generation for publication: Producing high-quality PDF figures for inclusion in scientific publications.

Methodology:

Implemented in Perl, leverages R for graphics, processes orthologues from reciprocal best BLAST hits, OrthoMCL, or DAGchainer, generates a configuration file on first run, and outputs PDF figures.