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Synteny Analysis - Usage Guide

Overview

Analyze genome collinearity and conserved gene order between species using MCScanX, SyRI, and JCVI for evolutionary and comparative genomics studies.

Prerequisites

# MCScanX (compile from source)
git clone https://github.com/wyp1125/MCScanX
cd MCScanX && make
export PATH=$PATH:$(pwd)

# SyRI for structural variants
pip install syri

# JCVI for visualization
pip install jcvi

# BLAST for homology search
conda install -c bioconda blast

Quick Start

Tell your AI agent what you want to do:

  • "Find syntenic blocks between human and mouse genomes"
  • "Detect whole-genome duplications in my plant genome"
  • "Identify chromosomal rearrangements between two assemblies"

Example Prompts

Basic Synteny

"Find collinear gene blocks between Arabidopsis and rice"

"Create a synteny dot plot comparing my two genomes"

WGD Detection

"Look for whole-genome duplication signatures in this genome"

"Calculate Ks distribution for syntenic gene pairs"

Structural Variants

"Identify inversions and translocations between reference and query"

"Find structural rearrangements between chromosome assemblies"

What the Agent Will Do

  1. Prepare genome and annotation files for analysis
  2. Run all-vs-all BLASTP for homology detection
  3. Identify collinear gene blocks with MCScanX
  4. Classify syntenic relationships (1:1, 1:many)
  5. Detect structural variants with SyRI if requested
  6. Calculate Ks for dating duplications
  7. Generate visualization plots

Tips

  • Block size - Minimum 5 genes per block reduces noise; use 10+ for stringent analysis
  • E-value - Use 1e-10 for close species, 1e-5 for distant comparisons
  • Ks saturation - Values >2 are unreliable; filter before interpretation
  • WGD peaks - Multiple Ks peaks suggest multiple WGD events
  • Visualization - JCVI produces publication-quality synteny plots