🧬Multiple Sequence Alignment Tool

CUSABIO's Multiple Sequence Alignment (MSA) tool is a lightweight, browser-based application designed for fast and accurate alignment of nucleotide or amino acid sequences.

Whether you're analyzing gene variants, comparing protein homologs, or identifying conserved motifs across species, this tool provides a convenient and efficient way to perform small-to-medium scale alignments without the need for software installation.

The tool supports standard FASTA format, supports both DNA and protein sequences, and clearly marks non-identical positions across aligned sequences — helping users easily identify mutations, insertions, and deletions.

🔧Try the Tool Now

📍 Please input sequences. Each sequence should include a name and sequence content, as shown below:

🧭How to Use the MSA Tool?

Want a quick walkthrough? This short video shows how to input sequences, run the alignment, and interpret the results.

🔬Applications

This MSA tool is ideal for basic research and everyday sequence analysis tasks, including:

• 🧬 Comparative sequence analysis
• 🔍 Conserved motif identification
• 🧪 Primer or probe design
• 🌿 Molecular evolution and phylogenetics
• 🧫 Protein engineering and epitope mapping

❓Frequently Asked Questions

Q: Can I align both DNA and protein sequences?

A: Yes, but not in the same run. Please align DNA and protein sequences separately.

Q: Can I download the alignment result?

A: Currently, you can copy the output manually. Export features are under development.

Q: Are there any limitations for this tool?

A: Yes. Each sequence should not exceed 5,000 residues.

Q: Is this tool free to use?

A: Yes, CUSABIO provides this tool as a free resource for the research community.

📬Feedback

If you encounter issues or have suggestions for improvement, feel free to contact us at [email protected].