Tools - Pan-Web Single Genome Analyzer

Unique Gene Finder

Primary workflow (upload → compare → annotate)

Runs the core pipeline that classifies genes into core, accessory, and unique buckets using the selected pan-genome reference. Outputs FASTA files, summaries, and download bundles.

Same Celery comparison job exposed on the dashboard.
Stores every run under your account for later download.
Works with all registered pan-genomes.

Open Workflow

Optional Steps

Include annotation Runs eggNOG-mapper after gene classification.

Visualise annotation results Adds the visualization script after annotation.

Toggle a step to see which scripts will execute.

Unique Gene Search for Species / Strain ID

Reuse the pipeline twice and compare unique counts.

Upload your genome or use an existing genome ID, then compare it against two different pan-genomes. The system will show you how many unique genes your genome has compared to each species, helping you identify which species/strain your genome is closest to.

Tip: The species with fewer unique genes is likely a closer match to your genome.

Input File Type

CDS (Coding Sequences)

Genomic (Will run Prokka)

Select CDS if your file contains coding sequences, or Genomic if you want Prokka to generate CDS first

Upload Genome FASTA File Upload a new genome file (.fasta, .fa, .fna)

OR Use Existing Genome ID If you already uploaded a genome, enter its ID here

Note: Either upload a file OR provide a genome ID. If both are provided, the file upload will be used.

Target A

Species Pan-genome

Target B

Species Pan-genome

Compares your genome against both species Shows unique gene counts for species/strain identification

Fast ANI

Average nucleotide identity screening for species/strain identification

FastANI computes Average Nucleotide Identity (ANI) between your query genome and reference genome. Input: Upload your query genome FASTA file (.fasta, .fa, .fna) and your reference genome FASTA file. Output: ANI percentage, aligned fragments, and coverage for the comparison.

How it works: FastANI requires complete assembled genome FASTA files. Upload both your query genome and reference genome files directly - no database selection needed.

Important: Do NOT upload:

Gene/protein sequences (e.g., core_genes.fasta, accessory_genes.fasta)
Annotated genes or CDS sequences
Pan-genome gene collections

FastANI requires whole genome assemblies (contigs/scaffolds), typically several megabases in size.

Upload Query Genome FASTA File Upload your query genome file (.fasta, .fa, .fna)

Upload Reference Genome FASTA File Upload your reference genome file (.fasta, .fa, .fna)

CPU Threads Number of CPU threads to use for computation