Introduction
A comprehensive guide to using CHITRA for analyzing chromosomal rearrangements
CHITRA
The Chromosome Interactive Tool for Rearrangement Analysis (CHITRA) is an advanced bioinformatics tool designed to study chromosomal rearrangements by providing detailed and interactive visualizations of synteny blocks and chromosome breakpoints. This tool is a powerful resource for investigating evolutionary dynamics across multiple genomes.
Workflow Diagram
The CHITRA workflow integrates multiple data inputs to produce comprehensive visualizations:
- Input Data: Synteny data, Species data, and Reference sizes are the core inputs.
- Optional Inputs: Gene annotations and Breakpoints enrich the visualization.
- Processing: The system processes these files to map coordinates and identify syntenic regions.
- Visualization: Outputs include Linear Views and Circular Chord Maps.
Features
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Synteny Block Visualization: Conserved regions of chromosomes between different genomes can be visualised and easy to analyse in forward and reverse direction
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Chromosome Breakpoint Analysis: Breakpoints are mapped and visualized to help researchers identify evolutionary events and their impact on genome organization
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User-Friendly Visualization: Users can dynamically adjust views, compare genomes, and zoom into specific chromosomal regions of interest
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Multi-format Data Export: Supports export of visualizations (SVG, PNG, JPG) and data tables (CSV) for further analysis
What are Synteny Blocks?
A synteny block refers to a conserved segment of a genome where genes or sequences are found in the same relative order and orientation across different genomic strains. These blocks provide insights into the evolutionary relationships between genomes, helping researchers understand genomic rearrangements, speciation, and structural changes.
