arman-bio-msa

Create a bioinformatics tool called 'SequenceAligner' that utilizes the 'arman-bio-msa' package to perform multiple sequence alignments using the Needleman-Wunsch algorithm. This tool will allow users to input two or more biological sequences (DNA, RNA, or protein) and receive an aligned output, along with visual representations of the alignment process and results. Here’s a detailed breakdown of the steps and features your application should include:

1. **User Interface**: Develop a simple yet intuitive web-based user interface where users can input their sequences. Provide options for users to upload files in FASTA format or directly enter sequences into text fields.
2. **Sequence Input Validation**: Ensure that the sequences provided by the user are valid (e.g., correct nucleotide or amino acid characters). If invalid, notify the user with an error message.
3. **Alignment Execution**: Use the 'arman-bio-msa' package to execute the alignment process. The package should handle the dynamic programming aspect, but you need to set up the scoring matrix and gap penalties according to user preferences or default settings.
4. **Alignment Visualization**: Implement a feature that visualizes the alignment results in a graphical format. Users should be able to see the aligned sequences side by side, with mismatches, gaps, and matches clearly marked.
5. **Result Export**: Allow users to download the aligned sequences in various formats (e.g., FASTA, plain text).
6. **Help and Documentation**: Include comprehensive documentation explaining how to use the tool, including examples of valid input and expected output formats.
7. **Testing and Validation**: Write tests to ensure that the tool works correctly under different scenarios, such as varying sequence lengths, types, and content.
8. **Optional Features**:
   - Support for custom scoring matrices and gap penalties.
   - An option for users to compare their aligned sequences against known databases or reference sequences.
   - A feature that predicts possible mutations based on the alignment results.
9. **Deployment**: Plan for deployment on a cloud platform like Heroku or AWS, ensuring that the application is accessible over the internet.

Your goal is to create a robust, user-friendly tool that leverages the power of 'arman-bio-msa' to provide valuable insights into sequence alignments.