EFI - Chemically-Guided Functional Profiling

This web resource is supported by a Research Resource from the National Institute of General Medical Sciences (R24GM141196-01).

The tools are available without charge or license to both academic and commercial users.

Update of EFI Tools

The EFI Tools are being upgraded on 10/26/26. The site will not be available from 10/23-10/26 for maintenance.

While the updated site is functionally identical to the old site, jobs run prior to that date will only be available through the results link in the finalization email (not the Previous Jobs tab). User accounts created on the old site will no longer be available, and users are encouraged to create new accounts when the upgraded site becomes available.

This site uses the CGFP-ShortBRED programs (https://github.com/biobakery/shortbred and http://huttenhower.sph.harvard.edu/shortbred).

For more information on CGFP-ShortBRED, see

Levin, B. J., Huang, Y. Y., Peck, S. C., Wei, Y., Martínez-del Campo, A., Marks, J. A., Franzosa, E. A., Huttenhower, C., Balskus, E. P. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science 355, eaai8386 (2017). (DOI: 10.1126/science.aai8386)

For more information on ShortBRED, see

Kaminski J., Gibson M. K., Franzosa E. A., Segata N., Dantas G., Huttenhower C. High-specificity targeted functional profiling in microbial communities with ShortBRED. PLoS Comput Biol. 2015 Dec 18;11(12):e1004557. DOI: 10.1371/journal.pcbi.1004557

These programs use data computed by MicrobeCensus.

Nayfach, S. and Pollard, K.S. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biology 2015;16(1):51.

Portions of the metagenome data used on this site come from the Human Microbiome Project.

The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (14 June 2012). DOI: 10.1038/nature11234

The Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215-221 (14 June 2012). DOI: 10.1038/nature11209

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