ShinySyn

ShinySyn visualizes synteny and chromosome collinearity across genomes to support comparative genomics analyses.

Key Features:

• Interactive visualization: Dynamic visualization of macro-synteny and micro-synteny showing synteny blocks and gene pairs within and between species.
• Dynamic zooming: Seamless transition from genome-wide (macro-synteny) views to detailed gene-level representations of homologous genes.
• Genome-level dot plots: Generation of genome-wide dot plots to display chromosomal arrangements and conserved regions across entire genomes.
• MCscan integration: Built on the MCscan framework to perform collinearity and synteny detection analyses.

Scientific Applications:

• Comparative genomics: Investigation of chromosome collinearity and gene conservation across species.
• Evolutionary analysis: Exploration of evolutionary relationships and identification of conserved genomic regions.
• Structural variation analysis: Detection and interpretation of structural variations through synteny patterns.
• Plant genomics: Application of synteny analysis to plant genome studies.

Methodology:

Built on the MCscan framework and leveraging established MCscan algorithms for synteny detection.