Key Features
1. Pangenome Projection of a Single-Genome
Classifies genes from a single genome as core, accessory, cloud, or unique by mapping them to a curated species pangenome. Full context without multi-genome builds.
2. Unique Gene Finder
Strict validation thresholds (≥90% identity and ≥90% coverage) to find unique genes, generating clean FASTA collections and structured logs.
3. GeneEye Visualization Module
Publication-ready summary dashboards combining gene classification and EggNOG annotations with distribution graphs, bar charts, and tabular outputs.
4. Curated Pangenome Database
Built-in database of 1,801 bacterial species-level pangenomes. Constructed from clean assemblies, uniformly reannotated, and filtered for accuracy.
5. Reproducible Pipeline
Standardized pipeline (Prokka → Unique Gene Finder → EggNOG-mapper → GeneEye) executed in a secure server-side container.
6. Fully Web-Based Execution
Runs completely in the cloud. No dependencies, installations, command line instructions, or specialized hardware needed.
How It Works
Upload
Genome assembly in FASTA format
Reannotation
Parsed and prepared with Prokka
Classification
Unique Gene Finder maps sequences to references
Annotation
EggNOG maps pathways and classifications
Visualization
GeneEye formats classification outputs
Downloads
Save result FASTA archives and Excel spreadsheets
Applications
Rapid Contextualization
of newly sequenced clinical and environmental isolates
Unique Gene Search
Find species-specific markers or accessory traits
Functional Profiles
Map pathways and features of pangenome segments
Scientific Reporting
Generate figures and metadata summaries for papers
Tailored for clinical, research, academic, and industrial microbiology workspaces.