SynFind

SynFind identifies conserved syntenic regions across a query genome and multiple target genomes to predict orthologous and homeologous gene positions and support comparative and functional genomics analyses.

Key Features:

• Comprehensive synteny analysis: Identifies conserved syntenic regions across any set of target genomes given a query genome, enabling prediction of orthologous and homeologous gene locations even when genes are absent.
• Scalability for pairwise and multi-genome comparisons: Supports pairwise comparisons and large-scale analyses across many genomes to study genome evolution, gene loss, and transposition dynamics.
• Per-gene and genome-wide reporting: Produces detailed per-gene output and genome-wide datasets including syntenic gene locations and predicted gene positions.
• Functional homolog inference: Infers syntenic homologs to facilitate correlation of functional changes around genes between related organisms.
• Computational infrastructure and reproducibility: Operates within the CoGe job execution framework, providing scalable execution and support for multiple releases of the same organism.

Scientific Applications:

• Gene family studies: Enables investigation of evolutionary relationships and conservation within specific gene families using syntenic context.
• Genome-scale comparative analyses: Supports analyses of genomic architecture, evolution, and patterns of gene loss and transposition across species.
• Functional genomics: Facilitates study of functional changes and evolutionary pressures around genes by linking synteny with putative homologs.

Methodology:

Compares a query genome against multiple target genomes to identify conserved syntenic regions, with computations executed through the CoGe job execution framework.