Are you a researcher working with protein sequences? If so, you know the importance of accurately studying the effects of missense variants. However, converting these variants from their Human Genome Variation Society (HGVS) notation to FASTA format can be a time-consuming task. But fear not, because there's now a Python script available that I personally designed to tackle this challenge!
Here is the GitHub link: https://github.com/karagol-taner/HGVS-missense-variants-to-FASTA
Whether you're exploring single variants or handling large lists, my tool simplifies the process, saving you valuable time for your research. Simply input the required information, including the protein or gene name, wild-type sequence, variant notations, and the desired filename for the output FASTA file. The script handles both manual input and file input, making it adaptable to your workflow.
You have three options for running the script:
Option 1 (RECOMMENDED, for all platforms): If you have Python 3.x installed on your system, simply utilize pip to install the package and start using the command HGVStoFASTA immediately:
pip install HGVStoFASTA
HGVStoFASTAOption 2 (for all platforms): Prefer a cloud-based solution? You can run the script directly from Google Colab: Access the script directly on Google Colab
Option 3 (for Windows): You can directly run this .EXE file.
Input Types for Variants
The script supports both manual input and file input for variant notations. Whether you prefer typing them out or importing from a text file, the choice is yours. Just ensure the variant notations follow the specified format for nucleotide or amino acid sequences.
Review, Save, and View Results
Before proceeding, review the entered information for accuracy. Once confirmed, the script will generate the variant sequences and save them to the specified file in FASTA format. After execution, it will automatically open the generated FASTA file for viewing using your system's default application.
Questions and Support
Got questions or encountered issues? Don't hesitate to reach out! I'm here to provide assistance every step of the way.
Screenshot of the script in action
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