amypred

Snakemake pipeline to perform amyloid prediction on a set of proteins in fasta format.

Usage

Put the target files with the extension ".faa" in the folder samples and run: snakemake -j <cores>

Requirements

• Snakemake
• R
• AmyloGram
• APPNN

Output

The output is created in the results folder and consists of a ".csv" file where the rows are the proteins in the file and the columns the prediction scores.

References

• Fernandez-Escamilla, A.-M., Rousseau, F., Schymkowitz, J. & Serrano, L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22, 1302–1306 (2004).
• Família, C., Dennison, S. R., Quintas, A. & Phoenix, D. A. Prediction of Peptide and Protein Propensity for Amyloid Formation. Plos One 10, e0134679 (2015).
• Burdukiewicz, M. et al. Amyloidogenic motifs revealed by n-gram analysis. Sci Rep-uk 7, 12961 (2017).