SynChr

SynChr reconstructs and visualizes synteny blocks across eukaryotic genomes to support comparative genomics analyses such as genome (re-)annotation, detection of duplicated regions and whole-genome duplications, and estimation of rearrangement rates.

Key Features:

• Reciprocal Best-Hits (RBH) algorithm: Calculates Reciprocal Best-Hits (RBH) to establish the core structure of synteny blocks.
• Inclusion of non-RBH homologs: Enhances synteny blocks by incorporating non-RBH syntenic homologs.
• Single-workflow implementation: Integrates all necessary computational steps and accepts a single synteny block stringency parameter, eliminating the need for preliminary tools such as Blast or TribeMCL.
• Performance benchmarking: Demonstrated faster runtime than MCScanX and i-ADHoRe while maintaining at least equivalent synteny reconstruction performance.
• Optimization for large genomes: Optimized for speed on standard desktop computers and applicable to large eukaryotic genomes such as human.
• Comprehensive visualization outputs: Produces dotplots, chromosome paintings, and detailed synteny maps that display homology relationships, synteny breakpoints, and included genetic features.

Scientific Applications:

• Comparative genomics: Reconstruction and visualization of synteny blocks to inform genome (re-)annotation, identify duplicated regions, detect whole-genome duplication events, and estimate rearrangement rates.
• Cross-species synteny analysis: Applicable to analyses across different levels of synteny conservation, with benchmarking on pairwise comparisons such as Human/Mouse, Human/Zebra Finch, and Human/Zebrafish.

Methodology:

Computes Reciprocal Best-Hits (RBH) to define core synteny block structure and integrates non-RBH syntenic homologs within a single-workflow implementation that uses a synteny block stringency parameter.