User Guide

Step-by-step instructions for using the Pan-Web Single Genome Analyzer

Quick Start Guide

  1. Navigate to the Dashboard and go to the "Pan-Genome Comparison" tab
  2. Click "Choose File" and select your FASTA file
  3. Optionally fill in organism name, strain, and description
  4. Click "Upload Genome"
  5. Wait for the upload confirmation message
Tip: Supported formats: .fasta, .fa, .fna (Max size: 200MB)

  1. In the "Select Species and Pan-Genome" section
  2. Choose a Species from the dropdown menu
  3. Select a Pan-Genome from the available options
  4. The "Start Comparison" button will become enabled

Make sure to select a species first to see available pan-genomes.

  1. Click the "Start Comparison" button
  2. Monitor the progress in the status section
  3. Wait for the analysis to complete (typically 2-20 minutes)
  4. Results will appear automatically when ready
Note: Large genomes may take longer. Please be patient.

  • Metrics: View total, core, accessory, and unique gene counts
  • Visualizations: Explore Venn diagrams and gene previews
  • COG Charts: View functional classification pie charts
  • Downloads: Download FASTA files, Excel annotations, and charts

All results are available in the "Results & Downloads" tab.

Supported File Formats

Input Formats
  • .fasta - Standard FASTA format
  • .fa - FASTA format
  • .fna - Nucleotide FASTA
Maximum file size: 200MB
Output Formats
  • .fasta - Gene sequences (Core, Accessory, Unique)
  • .xlsx - Excel annotations with COG categories
  • .png - COG classification pie charts
  • .txt - Summary and mapping files

Tutorial Guide

Download our comprehensive tutorial presentation to learn how to use PanWSGA step-by-step. This PDF guide covers all features and workflows of the platform.

  • Complete walkthrough of all features
  • Step-by-step instructions with screenshots
  • Tips and best practices
Download Tutorial PDF PDF Format

Troubleshooting

  • Check file size (must be under 200MB)
  • Verify file format (.fasta, .fa, or .fna)
  • Ensure file is not corrupted
  • Check your internet connection

  • Large genomes (10,000+ genes) may take 2-20 minutes
  • Annotation step typically takes 2-20 minutes
  • Check the status indicator for current progress
  • If stuck for over 1 hour, try refreshing the page

  • Wait for the analysis to complete (check status)
  • Refresh the page if status shows "completed"
  • Check browser console for errors (F12)
  • Try logging out and back in

  • Ensure annotation completed successfully
  • Check that Excel files were generated
  • Verify COG_category column exists in annotations
  • Wait a few minutes for chart generation

Tips & Best Practices

Best Practices
  • Use properly formatted FASTA files
  • Include organism name for better results
  • Ensure sequences are complete and valid
  • Select appropriate species for comparison
  • Save your results regularly
Pro Tips
  • Start with smaller genomes for testing
  • Use descriptive filenames for easy tracking
  • Download results immediately after completion
  • Check COG categories for functional insights
  • Compare multiple genomes for better analysis