PTM Position Remapping

Version: 1.0.0

Commit Hash: 4c6fa509a7938878f993e5be2df2fc7ffd74b6c3

Author: Cauldron Team

Category: utilities

Remap PTM positions from peptides to protein sequences using UniProt data

Install with Cauldron get_app
README

PTM Position Remapping

Installation

⬇️ Click here to install in Cauldron (requires Cauldron to be running)

Repository: https://github.com/noatgnu/ptm-remap-plugin

Manual installation:

  1. Open Cauldron
  2. Go to Plugins → Install from Repository
  3. Paste: https://github.com/noatgnu/ptm-remap-plugin
  4. Click Install

ID: ptm-remap
Version: 1.0.0
Category: utilities
Author: Cauldron Team

Description

Remap PTM positions from peptides to protein sequences using UniProt data

Runtime

  • Environments: python

  • Entrypoint: remap_ptm.py

Inputs

Name Label Type Required Default Visibility
input_file Input File file Yes - Always visible
peptide_column Peptide Sequence Column column Yes - Always visible
position_in_peptide_column Position in Peptide Column column Yes - Always visible
uniprot_acc_column UniProt Accession Column column Yes - Always visible
fasta_file FASTA File (Optional) file No - Always visible

Input Details

Input File (input_file)

Tab-separated or CSV file containing peptide data

Peptide Sequence Column (peptide_column)

Column containing peptide sequences

Position in Peptide Column (position_in_peptide_column)

Column containing the position of the PTM within the peptide

UniProt Accession Column (uniprot_acc_column)

Column containing UniProt accession IDs

FASTA File (Optional) (fasta_file)

Optional FASTA file with protein sequences. If not provided, sequences will be fetched from UniProt.

Outputs

Name File Type Format Description
remapped_peptides.txt remapped_peptides.txt data Tab-separated file with remapped PTM positions

Requirements

  • Python Version: >=3.10

Python Dependencies (External File)

Dependencies are defined in: requirements.txt

  • pandas>=2.0.0
  • click>=8.0.0
  • uniprotparser>=1.0.0

Note: When you create a custom environment for this plugin, these dependencies will be automatically installed.

Usage

Via UI

  1. Navigate to utilities → PTM Position Remapping
  2. Fill in the required inputs
  3. Click Run Analysis

Via Plugin System

const jobId = await pluginService.executePlugin('ptm-remap', {
  // Add parameters here
});