ampir: Antimicrobial Peptide Prediction in R

ampir (short for antimicrobial peptide prediction in r ) identifies antimicrobial peptides (AMPs) based on physico-chemical properties of amino acid sequences. It is optimised for scanning large collections of sequences (eg the predicted proteome for an organism) to identify a suite of putative AMPs.

ampir was developed by Legana Fingerhut and Ira Cooke in the Marine Omics and Marine Molecular Biology labs at James Cook University. It is open source and available for use via this web page or as an R package.

If you use ampir in your research please cite the following paper

Fingerhut, L.C.H.W., Miller, D.J., Strugnell, J.M., Daly, N.L., Cooke, I.R., 2020. ampir: an R package for fast genome-wide prediction of antimicrobial peptides. Bioinformatics.

Usage Instructions

Select the classification model

For best results it is important to select the model that accurately represents your sequence type.

  • For collections of full length proteins you should select the precursor model. This is the most common situation when working with predicted proteins from a translated transcriptome or translated gene models.
  • The alternative model (mature) is best suited for sequences representing the final AMP sequence after post-translational processing (eg removal of N-terminal signal and pro-peptide sequences). This situation is commonly encountered if your sequences were obtained through direct proteomic sequencing of native material (eg Edman sequencing or mass spectrometry)

Enter protein sequences in fasta format

You may either paste sequences into the text box below (suitable for small searches) or upload a file containing your sequences