About

Functionality

AMPcombi is developed by an interdisciplinary team to:

• Parse and filter the output of the following AMP prediction tools:

  Tool	Version
  Ampir	1.1.0
  AMPlify	1.0.3
  Macrel	1.1.0
  HMMsearch	3.3.2
  EnsembleAMPpred	latest
  NeuBI	latest
  AMPgram	latest
  AMPtransformer	latest

• Annotate the recovered AMPs by alignment to curated or experimentally validated AMP reference databases using MMSeqs2 search v.15.6f452:

  Tool	Version
  DRAMP	4.0 (general AMPs)
  APD	09142020
  UniRef100	2024_05 (mmseqs version)

  💡 If no database is provided by the user, AMPcombi will automatically download the DRAMP db and use it for classification.

  Note

  Databases undergo a cleaning step after downloading that ensures only valid AMP sequences (remove those with characters not included in the amino acid alphabet) are used for alignment.

• Estimate and calculate the corresponding molecular weight, isoelectric point, hydrophobicity, pH, and the fraction of helix turns and beta sheets using:

  Tool	Version
  BioPython - ProteinAnalysis	1.80

  💡 Any transporter gene present in the vicinity of the AMP on the contig is also reported.

• Extensively filter the recovered AMP hits based on their lengths, probability scores, E-values, and the presence of stop codons downstream and upstream of the AMP hit on the contig.

  💡 If extra contig or sample metadata is available, these can further be added to the final filtered table, for example, sample metadata, pydamage, contig taxonomic classification, etc. 💡 If the user provides output files generated by interproscan, hits with specific domains can further be removed from the final table. An example for how to run InterProscan can be found in Test runs.

• Cluster the predicted AMPs and filter them by removing singletons, clusters with a minimum number of members, or clusters from one label. This is primarily carried out using:

  Tool	Version
  MMseqs2	15.6f452

• Predict extracellular AMPs, provided the user installs SignalP separately. For licensing issues, SignalP can only be downloaded and used by academic users; other users are requested to contact DTU Health Technology Software Package before using it. Please refer to the SignalP documentation for further details.

  Tool	Version
  SignalP	6.0

• Visualize results: a Shiny app is accessible through ./pyshiny. This is a visualisation dashboard that renders the AMPcombi final summary table, allowing for data exploration and visualization (see: Visualization).

  Tool	Version
  Shiny	0.7.1

Authors

The tool was initiated by @louperelo and expanded by @darcy220606 with major design and scientific contributions from @RosaLuzia. @jasmezz is involved in maintenance.

Funding

This project was funded by Werner Siemens Foundation grant ‘Paleobiotechnology’.