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 species.

Features

1. Synteny Block Visualization: Conserved regions of chromosomes between different species can be visualised and easy to analyse in forward and inverse direction

2. Chromosome Breakpoint Analysis: Breakpoints are mapped and visualized to help researchers identify evolutionary events and their impact on genome organization

3. Evolutionary Insights: By analyzing the rearrangement patterns, it supports hypotheses about evolutionary pressures and genetic innovations

4. User-Friendly Visualization: Users can dynamically adjust views, compare species, and zoom into specific chromosomal regions of interest

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 species or strains. These blocks provide insights into the evolutionary relationships between organisms, helping researchers understand genomic rearrangements, speciation, and structural changes.

HOW TO USE CHITRA?

Below are the step-by-step instructions, accompanied by pictorial representations, to ensure a seamless experience with CHITRA.

Step 1: Getting Started

• On the landing page, click the “Get Started” button to begin.

Step 2: Uploading Files or Viewing Example Data

• On the next page, you can either:

1. Upload Files
2. View Example Datasets

2.1.1 File Upload Instructions

Mandatory Input Files:

1. Synteny Data
2. Species Data
3. Reference Chromosome Size

Optional Input Files:

1. Gene Annotations
2. Breakpoint Data

To upload files:

Click the “Upload Data” button. A popup window will appear where you can browse and upload the required input files.

Note: All input files should be in CSV format

2.1.2 Using Example Datasets

CHITRA includes pre-loaded example datasets to help users explore its functionality. Three types of example datasets are available:

1. Basic Synteny

   • Visualize synteny blocks among three species.
   • Input files required:
     • synteny_data.csv
     • species_data.csv
     • reference_chromosome_sizes.csv

2. Multiple Synteny

   • Compare synteny blocks among multiple species

   • Input files required same as Basic Synteny

     • ref_gene_annotations.csv
     • breakpoints.csv

3. Annotated Genome

• Analyze annotated genomes using real datasets.

• Input files required here are the same as for Multiple Synteny with two more additional files

  • ref_gene_annotations.csv
  • breakpoints.csv