FANTASIA
========

**Functional ANnoTAtion based on embedding space SImilArity**

FANTASIA is an advanced pipeline designed for automatic functional annotation of protein sequences using state-of-the-art protein language models. It integrates deep learning embeddings and similarity searches in vector databases to associate Gene Ontology (GO) terms with proteins.

.. toctree::
   :maxdepth: 2
   :caption: Contents

   key_features
   data_source
   method
   performance
   acknowledgments
   citing_fantasia
   contact

.. toctree::
   :maxdepth: 2
   :caption: Use cases

   benchmarking
   functional_annotation


.. toctree::
   :maxdepth: 2
   :caption: Deployment

   dev_deployment
   prod_deployment
   docker_publish
   slurm.rst


.. toctree::
   :maxdepth: 2
   :caption: Help

   faq