Welcome to modlAMP’s documentation!

modlAMP

Authors: Alex Müller, Gisela Gabernet

Copyright: (c) 2016 - 2021 ETH Zurich, Switzerland; Alex Müller, Gisela Gabernet, Gisbert Schneider (modlab).

This is a Python package (for Python 3 since version 4.0.0) that was designed for working with peptides, proteins or any sequence of natural amino acids. It incorporates several modules, like sequence generation (module sequences), sequence library analysis (module analysis) or descriptor calculation (module descriptors). For basic instructions on how to use the package, check the README or the example script. The project’s GitHub page can be found here: http://github.com/alexarnimueller/modlamp

The package has the following contents:

• 1. README
  • 1.1. Installation
  • 1.2. Usage
    • 1.2.1. Importing modules
    • 1.2.2. Generating Sequences
    • 1.2.3. Calculating Descriptor Values
    • 1.2.4. Plotting Features
    • 1.2.5. Database Connection
    • 1.2.6. Loading Prepared Datasets
    • 1.2.7. Analysing Wetlab Circular Dichroism Data
    • 1.2.8. Analysis of Different Sequence Libraries
    • 1.2.9. Documentation
    • 1.2.10. Citing modlAMP
• 2. Package Documentation
  • 2.1. modlamp.descriptors
  • 2.2. modlamp.sequences
  • 2.3. modlamp.database
  • 2.4. modlamp.datasets
  • 2.5. modlamp.plot
  • 2.6. modlamp.ml
  • 2.7. modlamp.wetlab
  • 2.8. modlamp.analysis
  • 2.9. modlamp.core
• 3. Example scripts
  • 3.1. A modlamp example script for peptide classification with a Random Forest classifier.
  • 3.2. An alternative example for single peptide classification with a RF classifier.
  • 3.3. Loading sequences from a FASTA file
  • 3.4. Combining different descriptors & saving to csv
• 4. LICENSE
• 5. TODOs

If you use modlAMP in a scientific publication, we would appreciate citations to the following paper:

Müller A. T. et al. (2017) modlAMP: Python for anitmicrobial peptides, Bioinformatics 33, (17), 2753-2755, DOI:10.1093/bioinformatics/btx285.

Indices and tables

• Index

• Module Index

• Search Page