DNA/RNA Frame Translation

Version: 1.0.0

Commit Hash: a349fe3dcbd17f0dd327cacabaf5b3eca331b1d9

Author: Toan Phung

Category: proteomics

Subcategory: sequence-analysis

Translates DNA/RNA sequences to amino acid sequences using 3-frame or 6-frame translation. Supports custom start/stop codons or translation from position 0. Useful for proteogenomics, novel peptide discovery, and alternative splicing analysis.

Install with Cauldron get_app
README

DNA/RNA Frame Translation

Installation

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

Repository: https://github.com/noatgnu/dna-frame-translation-plugin

Manual installation:

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

ID: dna-frame-translation
Version: 1.0.0
Category: proteomics
Author: Toan Phung

Description

Translates DNA/RNA sequences to amino acid sequences using 3-frame or 6-frame translation. Supports custom start/stop codons or translation from position 0. Useful for proteogenomics, novel peptide discovery, and alternative splicing analysis.

Workflow Diagram

flowchart TD
    Start([Start]) --> step1
    step1[Parsing arguments...]
    step1 --> step2
    step2[Loading sequences...]
    step2 --> step3
    step3[Translating sequences...]
    step3 --> step4
    step4[Writing output files...]
    step4 --> step5
    step5[Translation completed successfully!]
    step5 --> End([End])

Runtime

  • Environments: python

  • Entrypoint: translation_runner.py

Inputs

Name Label Type Required Default Visibility
input_file Input Sequence File file Yes - Always visible
input_format Input Format select (auto, fasta, csv, tsv) Yes auto Always visible
sequence_column Sequence Column text No sequence Visible when input_format is one of: csv, tsv
id_column ID Column text No gene Visible when input_format is one of: csv, tsv
translation_mode Translation Mode select (three_frame, six_frame) Yes six_frame Always visible
use_start_codons Require Start Codon boolean No false Always visible
start_codons Start Codons text No ATG Visible when use_start_codons = true
use_stop_codons Stop at Stop Codon boolean No true Always visible
stop_codons Stop Codons text No TAA,TAG,TGA Visible when use_stop_codons = true
min_length Minimum Peptide Length number (min: 0, max: 10000, step: 1) No 0 Always visible
max_length Maximum Peptide Length number (min: 0, max: 100000, step: 1) No 0 Always visible
genetic_code Genetic Code Table select (1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33) No 1 Always visible

Input Details

Input Sequence File (input_file)

File containing DNA/RNA sequences (FASTA or tabular format)

Input Format (input_format)

Format of input file. 'auto' detects based on file extension.

  • Options: auto, fasta, csv, tsv

Sequence Column (sequence_column)

Column name containing sequences (for tabular input)

ID Column (id_column)

Column name for sequence identifiers (for tabular input)

Translation Mode (translation_mode)

3-frame (forward only) or 6-frame (forward + reverse complement)

  • Options: three_frame, six_frame

Require Start Codon (use_start_codons)

If enabled, translation starts from specified start codons. If disabled, translates from position 0 in each frame.

Start Codons (start_codons)

Comma-separated list of start codons (standard: ATG; alternatives: GTG, CTG, TTG, ACG)

  • Placeholder: ATG,GTG,CTG,TTG,ACG

Stop at Stop Codon (use_stop_codons)

If enabled, translation stops at specified stop codons. If disabled, translates entire frame (stop codons become *).

Stop Codons (stop_codons)

Comma-separated list of stop codons (standard: TAA, TAG, TGA)

  • Placeholder: TAA,TAG,TGA

Minimum Peptide Length (min_length)

Minimum amino acid length for output sequences (0 = no filter)

Maximum Peptide Length (max_length)

Maximum amino acid length for output sequences (0 = no limit)

Genetic Code Table (genetic_code)

NCBI genetic code table: 1=Standard, 2=Vertebrate Mito, 3=Yeast Mito, 4=Mold Mito, 5=Invertebrate Mito, 6=Ciliate, 9=Echinoderm Mito, 10=Euplotid, 11=Bacterial, 12=Alt Yeast, 13=Ascidian Mito, 14=Alt Flatworm Mito, 15=Blepharisma, 16=Chlorophycean Mito, 21-33=Various specialized codes

  • Options: 1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33

Outputs

Name File Type Format Description
translated_sequences translated_sequences.fasta data fasta Translated amino acid sequences in FASTA format
translation_summary translation_summary.tsv data tsv Summary table with sequence IDs, frames, lengths, and ORF positions
translation_report translation_report.txt report txt Summary statistics of the translation

Requirements

  • Python Version: >=3.11

Python Dependencies (External File)

Dependencies are defined in: requirements.txt

  • click>=8.0.0
  • biopython>=1.81
  • pandas>=2.0.0

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

Example Data

This plugin includes example data for testing:

  min_length: 20
  genetic_code: 1
  start_codons: ATG,GTG,CTG
  max_length: 0
  input_format: auto
  translation_mode: six_frame
  use_start_codons: false
  use_stop_codons: true
  stop_codons: TAA,TAG,TGA

Load example data by clicking the Load Example button in the UI.

Usage

Via UI

  1. Navigate to proteomics → DNA/RNA Frame Translation
  2. Fill in the required inputs
  3. Click Run Analysis

Via Plugin System

const jobId = await pluginService.executePlugin('dna-frame-translation', {
  // Add parameters here
});