FANTASIA (Functional ANnoTAtion based on embedding space SImilArity)
Pipeline for functional annotation of proteins using language models
Basic Information
| Repository | https://github.com/CBBIO/FANTASIA |
| Documentation | https://fantasia.readthedocs.io/en/latest/ |
| Seminar | Gemma I Mtnez (IBE, CSIC) present the tool FANTASIA |
| Main publication (DOI) |
10.1101/2024.02.28.582465
10.1101/2024.02.14.580341 |
| Contact email | frapercan1@alum.us.es, gemma.martinez@ibe.upf-csic.es, a.rojas.m@csic.es, rosa.fernandez@ibe.upf-csic.es |
| Authors/Maintainers | Ana Rojas |
| Type of application | Galaxy tool, Singularity container, Command line pipeline |
| Programming languages | PythonBASH / Shell |
| Keywords | Computational Methods, Data Analysis, Artificial Intelligence, Applications of Computational Biology, Model organisms, Large language models, Functional genomics, Functional annotation, Function prediction |
Technical details
| Input file formats | fasta |
| Output file formats | Other |
| Software compatibility | Linux |
| Hardware requirements | For an average peptide FASTA file containing 20k sequences it would need around 50Gb of RAM (the higher the number of sequences the higher the memory requirements). |
| Type of containerization | Singularity/AppTainer |
| Wrapper type | None |
| Compatible tools | Output files are already formatted to be used as input for topGO R package (GO enrichment). |
| Funding resource | National competitive funding, Regional/local competitive funding, Institutional funding, EU funding |
| Funding support | National competitive funding, Regional/local competitive funding, Institutional funding, EU funding |
Statistics
| Unique users (last 12 months) | <100 |
| Unique users (since first release) | <100 |
| Software downloads (last 12 months) | <100 |
| Software downloads (since first release) | <100 |
| Jobs submitted (last 12 months) | <100 |
| Jobs submitted (since first release) | <100 |
| Repository clones (last 12 months) | <100 |
| Repository clones (since first release) | <100 |
| Citations (last 12 months) | <100 (~4 as of 15/10/2026) |
| Citations (since first release) | <100 (13 as of 15/10/2026) |
| Early-stage researcher effort (development) | 1-2 |
| Early-stage researcher effort (maintenance) | 1 |
| Technician-supported effort (development) | 1-2 |
| Technician-supported effort (maintenance) | 1 |
| Other effort (development) | 0-1 |
| Other effort (maintenance) | |
| Total effort (development) | |
| Total effort (maintenance) |