🧬 Multiple Sequence Alignment (MSA) Tool
The Multiple Sequence Alignment (MSA) tool processes multiple DNA or protein sequences to identify regions of similarity, functional conservation, and evolutionary relationships. It utilizes the Neighbor-Joining algorithm to construct phylogenetic trees based on sequence distance.
1. Input and Actions
This section manages the sequence data used for alignment.
Input Area
The main input area accepts raw sequence data in FASTA format.
| Feature | Requirement | Description |
|---|---|---|
| Format | FASTA | Sequences must start with a header line (>Name) followed by the sequence data on subsequent lines. |
| Limit | Max 50 sequences | A constraint to ensure performance and manageable alignment visualization. |
| Data Type | DNA or Protein | The tool can handle both nucleic acid and amino acid sequences. |
Action Buttons
| Button | Function |
|---|---|
| Align Sequences | Executes the alignment algorithm (e.g., ClustalW, MUSCLE, or similar) on the provided FASTA input. |
| Clear | Clears the text editor of all input sequences. |
| Example | Pre-fills the input box with sample sequences to demonstrate the required FASTA format and provide a quick test case. |
2. Alignment Results
The results section displays the core alignment and calculated conservation measures.
Sequence Visualization
The alignment is presented with color-coding, where the same color indicates a match or a biochemically similar residue across all sequences.
- Sequence Identifiers: Each aligned sequence is listed with its original FASTA header (e.g.,
DH55|1:16707270-16708136). - Alignment Block: Shows the sequences lined up, with gaps introduced by the algorithm to maximize matching residues.
Conservation Metrics
A key output of the alignment is the measure of conservation, typically represented by two elements:
- Sequence Logo (Top): This track visually represents the most frequent residues (bases or amino acids) at each position. The height of the letter at any position indicates the level of conservation (information content) at that site.
- Conservation Bar (Bottom): A bar graph showing the conservation score across the alignment. Taller bars indicate positions where all or most sequences have the same residue (high conservation). This track is a direct indicator of potential functional or structural importance in that region.