Pairwise Sequence Alignment
FreeAlign two DNA/RNA sequences using global or local alignment algorithms
Pairwise Alignment aligns two sequences to identify regions of similarity. This is fundamental for:
- **Sequence similarity**: Measure how similar two sequences are - **Homology detection**: Identify evolutionarily related sequences - **Variant detection**: Find differences between sequences - **Functional annotation**: Transfer annotations between similar sequences
Alignment types
- **Global alignment**: Aligns entire sequences end-to-end - **Local alignment**: Finds best-matching subsequences
Required
- Two DNA or RNA sequences - Can be input as raw sequences or FASTA format
Parameters
- **Alignment Type**: Global or Local - **Global**: Best for similar-length sequences, aligns entire length - **Local**: Best for finding similar regions, handles length differences better
Example input
``` Sequence 1: ATGCGATCGATCG Sequence 2: ATGCGATCGATCA ```
Alignment Results
- **Aligned Sequence 1**: First sequence with gaps inserted - **Aligned Sequence 2**: Second sequence with gaps inserted - **Similarity Score**: Numerical score indicating sequence similarity - **Alignment Length**: Length of the aligned sequences - **Gaps**: Dashes (-) represent insertions/deletions
Interpretation
- Matches indicate identical nucleotides - Mismatches indicate substitutions - Gaps indicate insertions or deletions (indels) - Higher similarity scores indicate more similar sequences
**1. Sequence Comparison** - Compare gene sequences from different organisms - Identify orthologs and paralogs - Measure evolutionary distance
**2. Variant Analysis** - Find SNPs and indels - Compare sample to reference sequence - Identify sequence differences
**3. Functional Annotation** - Transfer functional annotations - Identify conserved functional domains - Predict gene function
1. **Choose alignment type**: Use global for full-length comparisons, local for finding similar regions 2. **Sequence quality**: Ensure high-quality sequences for accurate alignment 3. **Consider context**: Similarity thresholds vary by sequence type and application 4. **Gap interpretation**: Understand that gaps may represent real indels or alignment artifacts 5. **Multiple comparisons**: For multiple sequences, consider multiple sequence alignment tools