FAPROTAX is a computational tool that maps prokaryotic taxa (e.g. genera or species) to established metabolic or other ecologically relevant functions, using the current literature on cultured strains.
This website presents FAPROTAX v2, a major overhaul of the previously published FAPROTAX v1, with improved taxonomic breadth and resolution, greater flexibility in the functional prediction algorithms, adding support for functional annotation from 16S rRNA sequences, and incorporating the latest developments in species taxonomy and experimental literature.
FAPROTAX consists of a reference dataset, which contains experimentally confirmed phenotypic information on thousands of prokaryotic species, as well as a software for converting taxonomic microbial community profiles (e.g. in the form of an OTU table) into putative functional profiles.
Predictions account for both cultured and uncultured organisms/OTUs in each sample, based on their evolutionary relationships to cultured species.
FAPROTAX is a cheaper alternative to metagenomic sequencing, and can be a valuable alternative to gene-centric prediction tools such as PICRUSt.
Indeed, the information stored in the FAPROTAX database is experimentally confirmed, and the predictions of FAPROTAX are in terms of phenotypes/functions rather than gene content.
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FAPROTAX v2 facts
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Potential applications
- Ecological interpretation of 16S marker gene data.
- Cheaper alternative to environmental shotgun sequencing (metagenomics) for functional community profiling.
- Complementary to metagenomics, e.g. resolving ambiguities in the interpretation of community gene content.
- Rapid identification of taxonomic groups in a sample with particular metabolic phenotypes (e.g. all known or putative methanogens).
- Database can be used to train machine learning models for predicting phenotypes from genotypes.
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FAPROTAX-db
We also provide FAPROTAX-db, which is a database of experimentally validated species traits, for use as a standalone resource.
The FAPROTAX reference data (used for predictions) are a strict subset of FAPROTAX-db, essentially covering the subset of species for which we were able to retrieve high-quality full-length 16S rRNA sequences for building the reference tree.
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Access
FAPROTAX data and software are freely available here.
Please consult the License agreement prior to downloading FAPROTAX.
Please cite FAPROTAX if you use it for a scientific publication.
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