🔄 EMBOSS Backtranambig: Back-Translating Ambiguous DNA
EMBOSS Backtranambig is a bioinformatics tool used to back-translate a protein sequence into a degenerate nucleic acid sequence, specifically designed to handle ambiguous amino acid codes. This is useful for designing degenerate primers or probes when the exact DNA sequence encoding a protein is unknown.
❓ What is EMBOSS Backtranambig?
Backtranambig takes an amino acid sequence and generates all possible DNA sequences that could encode it, accounting for the degeneracy of the genetic code. It's particularly helpful when dealing with ambiguous protein residues (e.g., 'B' for Asp or Asn, 'Z' for Gln or Glu, 'X' for any amino acid), providing a comprehensive set of potential DNA sequences.
- Degenerate DNA Generation: Creates all possible DNA sequences from a protein.
- Ambiguity Handling: Explicitly supports ambiguous amino acid codes.
- Primer Design Aid: Generates sequences suitable for degenerate primer design.
🎯 Why Use Backtranambig? For Degenerate Primer Design & Probing
EMBOSS Backtranambig is indispensable for:
- 🔍 Degenerate Primer Design: Creating a set of degenerate oligonucleotide primers for PCR amplification when only a protein sequence is known.
- 🧬 Gene Isolation: Designing probes to isolate genes based on a known protein sequence.
- 📊 Sequence Cloning: Generating potential DNA sequences for gene synthesis or cloning strategies.
- 🎯 Cross-Species Homology: Inferring potential DNA sequences from a protein sequence to search for homologous genes in other organisms.
- 📈 Understanding Genetic Code Degeneracy: Visualizing the multiple codon possibilities for each amino acid.
🧑💻 How to Use EMBOSS Backtranambig on Job Dispatcher: A Step-by-Step Guide
Follow these simple steps to back-translate your protein sequence into ambiguous DNA:
1️⃣ Navigate to the Tool
- From the main menu, go to All Tools (or search for "EMBOSS Backtranambig").
- Click the prominent Use Tool button located next to "EMBOSS Backtranambig."
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.
>my_protein MKVLWAALLVTFLAGCQAImportant: 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 Backtranslation Job").
💡 Sequence Type: (Automatically set to Protein, as this tool processes protein sequences).
📚 CODON TABLE (
codontable): Select the genetic code table to use for back-translation.0(Standard Code) - Default2(Vertebrate Mitochondrial)3(Yeast Mitochondrial)4(Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma)5(Invertebrate Mitochondrial)6(Ciliate Macronuclear and Dasycladacean)9(Echinoderm Mitochondrial)10(Euplotid Nuclear)11(Bacterial)12(Alternative Yeast Nuclear)13(Ascidian Mitochondrial)14(Flatworm Mitochondrial)15(Blepharisma Macronuclear)16(Chlorophycean Mitochondrial)21(Trematode Mitochondrial)22(Scenedesmus obliquus)23(Thraustochytrium Mitochondrial)
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 degenerate nucleic acid sequence(s) corresponding to your input protein.
- The output will show ambiguous nucleotide characters (e.g., 'R' for A or G, 'Y' for C or T) where multiple codons can encode the same amino acid.
- ⭐ Tip: Use the output to design degenerate primers or probes, keeping in mind the level of degeneracy required for your specific application.
💬 Need Help?
If you run into issues, please visit our Contact Us page for support. Happy back-translating!