EFI-EST Tutorial

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.

Please cite your use of the EFI tools:

Rémi Zallot, Nils Oberg, and John A. Gerlt, The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways. Biochemistry 2019 58 (41), 4169-4182. https://doi.org/10.1021/acs.biochem.9b00735

Nils Oberg, Rémi Zallot, and John A. Gerlt, EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. J Mol Biol 2023. https://doi.org/10.1016/j.jmb.2023.168018

Tutorial Navigation:

References

1.Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC (2009) PLoS One 4, e4345.

2. Pythoscape: a framework for generation of large protein similarity networks. Barber AE 2nd, Babbitt PC (2012) Bioinformatics 28, 2845-6.

3. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Genome Res 13, 2498-504.

4. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Weizhong L, Godzik A (2006) Bioinformatics 22, 1658-9.

5. CD-HIT: accelerated for clustering the next generation sequencing data. Fu L, Niu B, Zhu Z, Wu S, Li W (2012) Bioinformatics 28, 3150-2.

6. Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL. (2015) Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics doi:10.1016/j.bbapap.2015.04.015