yascoma / epicurator

Epitopes Curation Tool

Epitopes Curation Tool

This tool consists of a set of filtering steps to enhance the discovery of new epitopes.

Requirements:

• External softwares needed:

  • ncbi-blast
  • mafft
  • BepiPred2.0

• Python packages needed:

  • os
  • scipy
  • numpy
  • Levenshtein
  • xml
  • statistics

Usage Instructions

• Preparation:

  1. git clone https://github.com/YasCoMa/EpiCurator.git
  2. cd EpiCurator
  3. unzip human_38_proteins
  4. move human_38_proteins.faa into the same directory as epicurator.py
  5. unzip lineages
  6. move lineages folder files into the same directory as epicurator.py
  7. unzip blastdb
  8. Go to EpiMiner folder to see its specific instructions, if you want to use it

• Pipeline parameters:

  • [function]
    Use to indicate the function you want to execute:
    1 - Analyze mutation details such as positions of AA modification
    2 - Compare overlapping and similarity between epitopes of distinct classes (I, II and B-cell) 3 - Validate epitopes occurrence in human genome and proteins 4 - Analyze epitopes provided by pdb structure and Discotope 5 - Analyze conservation of epitopes in lineages genome sequences and portions of genomes that they were in low, moderated or high coverage 6 - Check epitopes that are already published in IEDB database 7 - Calculate correlation between protein and epitope sizes 8 - Get epitopes coordinates in reference proteins 9 - Run bepipred 10 - Analyze output bepipred 11 - Get epitopes coordinates in genome

  • [file]
    File containing the epitopes separated by comma, with header in the following order (identification, epitope sequence and original protein/epitopes class (for function 2))
    This parameter is used in all functions except 4, 9 and 10

  • [folder]
    Used in functions 4, 9 and 10
    

• Running modes examples:

  1. Run mode 1:
     python3 epicurator.py [function] [file]

  2. Run mode 2:
     python3 epicurator.py [function] [folder]

Reference

Ferreira CS, Martins YC, Souza RC, Vasconcelos AT. EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes. PeerJ. 2021 Nov 30;9:e12548. https://peerj.com/articles/12548/

Bug Report

Please, use the Issue tab to report any bug.