Frequently Asked Questions

Find answers to common questions about the platform

General Questions

A pan-genome is the complete set of genes found across all strains of a species. It consists of:
  • Core genes: Present in all strains (essential functions)
  • Accessory genes: Present in some strains (variable functions)
  • Unique genes: Present in only one strain (strain-specific)

The platform supports standard FASTA formats:
  • .fasta - Standard FASTA format
  • .fa - FASTA format
  • .fna - Nucleotide FASTA format

Maximum file size: 200MB

Analysis time depends on genome size:
  • Small genomes (< 2,000 genes): 5-10 minutes
  • Medium genomes (2,000-5,000 genes): 10-15 minutes
  • Large genomes (> 5,000 genes): 15-30 minutes

The annotation step (eggNOG-mapper) typically takes 10-15 minutes and is optimized for speed.

Analysis & Results

COG (Clusters of Orthologous Groups) classification assigns genes to functional categories:
  • Information Storage & Processing: J (Translation), K (Transcription), L (Replication)
  • Cellular Processes: D (Cell cycle), M (Cell wall), O (Posttranslational modification)
  • Metabolism: C (Energy), E (Amino acids), G (Carbohydrates)
  • Poorly Characterized: R (General function), S (Unknown)

COG categories help understand the functional distribution of genes in your genome.

Genes are classified based on their presence in the reference pan-genome:
  • Core genes: Present in ≥95% of reference genomes (conserved across species)
  • Accessory genes: Present in 5-95% of reference genomes (variable presence)
  • Unique genes: Present in <5% of reference genomes (rare or novel)

This classification helps identify essential vs. variable genetic content.

Yes, you can download all results in multiple formats:
  • FASTA files: Core, Accessory, and Unique gene sequences
  • Excel files: Annotations with COG categories and functional information
  • Images: COG classification pie charts (.png)
  • Text files: Summary statistics and gene mappings

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

Technical Questions

The platform uses eggNOG-mapper for functional annotation:
  • DIAMOND for fast protein sequence alignment
  • eggNOG database (version 5.0) for orthology assignment
  • Prodigal for gene prediction (when needed)

All tools are optimized for speed while maintaining accuracy.

The platform works best with modern browsers:
  • Google Chrome (recommended)
  • Mozilla Firefox
  • Microsoft Edge
  • Safari (latest version)

Note: JavaScript must be enabled for full functionality.

If an analysis fails, try these steps:
  1. Check that your FASTA file is properly formatted
  2. Verify the file size is under 200MB
  3. Ensure you selected a valid species and pan-genome
  4. Try refreshing the page and running again
  5. Check the browser console (F12) for error messages

If problems persist, check the Help section for detailed troubleshooting.

Still have questions?

Check out our User Guide or contact support for assistance.

View User Guide