FORK
A reference-proteome analysis workspace built at the Comparative Genomics Lab (CGLab), IMBB-FORTH.
About the lab
The IMBB Comparative Genomics Lab (CGLab), led by Alexandros Pittis, combines comparative genomics, phylogenomics and single-cell transcriptomics to investigate how molecular and cellular complexity — particularly of the nervous system — emerges through evolution. The lab's work integrates protein-family analysis, transcriptional regulation, and nervous-system evolution with computational-biology approaches.
The lab is part of the Institute of Molecular Biology and Biotechnology (IMBB-FORTH) in Heraklion, Crete, within the Evolution, Development & Cell Biology division. Learn more at cgenomicslab.org.
About the tool
FORK is a Flask web app for querying, visualizing, and comparing proteins across a local UniProt Reference Proteomes database enriched with Pfam-A HMM search results. Once the database is set up, queries run entirely offline — no internet needed.
It provides three main analysis modules, plus sequence/domain utilities:
| Module | What you get |
|---|---|
| Phylogenetic Tree | Fetch sequences by Pfam/taxon → align (MAFFT) → tree (FastTree/IQ-TREE) → interactive D3 viewer or ETE4 explorer with domain shapes. |
| Presence / Absence | Taxa × Pfam profile heatmap; drill into any cell for sub-profiles or domain architecture breakdown. |
| High-Res Profile | Partition gene trees into subclade (paralog) groups — by depth, manual MRCA, node path, or automatic duplication detection — and profile each subclade separately across taxa. |
| Utilities | Standard retrieval, HMM search, accession lookup, domain coordinates, GO→domain profiles, and branch extraction. |