🔄 EMBOSS Backtranseq: Back-Translating Protein to DNA

EMBOSS Backtranseq is a bioinformatics tool used to back-translate a protein sequence into a nucleic acid sequence, typically DNA. Unlike Backtranambig, it focuses on generating a single, non-degenerate DNA sequence based on codon usage frequencies from a chosen species-specific codon usage table. This is highly useful for gene synthesis or cloning.

❓ What is EMBOSS Backtranseq?

Backtranseq takes an amino acid sequence and, using a selected codon usage table (often specific to a particular organism), generates a DNA sequence that is optimized for expression in that organism. It selects the most frequently used codon for each amino acid, aiming to produce a single, non-degenerate DNA sequence.

  • Codon Optimization: Generates DNA based on species-specific codon usage.
  • Non-Degenerate Output: Produces a single DNA sequence, not all possible variants.
  • Gene Synthesis Aid: Ideal for designing DNA sequences for expression.

🎯 Why Use Backtranseq? For Gene Synthesis & Expression Optimization

EMBOSS Backtranseq is indispensable for:

  • 🔍 Gene Synthesis: Designing the DNA sequence for a synthetic gene based on a desired protein sequence.
  • 🧬 Expression Optimization: Creating DNA sequences that are optimized for high expression levels in a specific host organism by using preferred codons.
  • 📊 Cloning Strategies: Generating DNA sequences suitable for cloning into expression vectors.
  • 🎯 Primer Design (Specific): Designing specific (non-degenerate) primers when the exact DNA sequence is being synthesized or targeted.
  • 📈 Understanding Codon Bias: Exploring the codon usage patterns of different organisms.

🧑‍💻 How to Use EMBOSS Backtranseq on Job Dispatcher: A Step-by-Step Guide

Follow these simple steps to back-translate your protein sequence to a codon-optimized DNA sequence:

1️⃣ Navigate to the Tool

  1. From the main menu, go to All Tools (or search for "EMBOSS Backtranseq").
  2. Click the prominent Use Tool button located next to "EMBOSS Backtranseq."

2️⃣ Input Your Protein Sequence

  • Locate the input box (large text area) or the "upload a Sequence File" option.

  • Paste your protein sequence(s) in FASTA format or upload a FASTA file.

    >ProteinA Alpha domain
MKVLWAALLVTFLAGCQAKVEQAV
>ProteinB Beta chain
GSHMLDPQFTNVYQGLRRSGFP
>ProteinC Gamma subunit
ACDEFGHIKLMNPQRSTVWY

  • Important: You can provide a sequence either by typing into the text area OR by uploading a file, but not both simultaneously. Please clear one input to proceed.

3️⃣ Configure Parameters

  • 📝 Title: Provide a descriptive title for your job (e.g., "My Codon Optimization Job").

  • 💡 Sequence Type: (Automatically set to Protein, as this tool processes protein sequences).

  • 📚 CODON TABLE (codontable): Select the species-specific codon usage table to use for back-translation. This is crucial for optimization.

    • Default: Ehuman.cut (Homo sapiens)
    • (Many other options available, e.g., for different bacteria, plants, animals, fungi, viruses, etc. Choose the one relevant to your target expression system.)

4️⃣ Submit Your Job

  • Once your sequence is entered and parameters are set, click the Submit or Run button.

  • Your job will be dispatched to the EMBL-EBI Web Service. You will be automatically redirected to a Job Status page to monitor its progress.

5️⃣ Interpret Results

  • On the results page, you will find the generated DNA sequence, optimized based on the selected codon usage table.
  • The output will be a single DNA sequence, with each amino acid translated to its most frequently used codon in the chosen organism.
  • ⭐ Tip: Always verify the generated DNA sequence against your desired protein sequence and consider any cloning restrictions or specific motifs needed for your downstream applications.

💬 Need Help?

If you run into issues, please visit our Contact Us page for support. Happy back-translating!