The Consensus Sequence tool generates a single representative sequence from multiple aligned DNA/RNA/protein sequences. The consensus sequence represents the most common nucleotide or amino acid at each position.
Applications
- Multiple sequence alignment analysis - Creating representative sequences - Sequence logo generation (visual representation) - Identifying conserved regions - Phylogenetic analysis preparation
Required format
- FASTA format with multiple sequences - Sequences must be aligned (same length)
Example input
``` >sequence1 ATGCGATCG >sequence2 ATGCGATCA >sequence3 ATGCGATCG ```
Sequence requirements
- All sequences must have the same length - Sequences should be pre-aligned - Supports DNA, RNA, and protein sequences
The consensus sequence is generated using majority rule:
Consensus generation
- At each position, the most frequent nucleotide/amino acid is selected - In case of ties, one character is chosen based on frequency - Gaps may be included if specified
Output includes
- Consensus sequence in FASTA format - Original sequences for reference - Position-wise frequency information (if available)
**1. Multiple Sequence Alignment Analysis** - Generate representative sequences from alignments - Identify conserved regions - Create sequence logos
**2. Phylogenetic Analysis** - Prepare sequences for tree construction - Reduce sequence complexity - Identify shared ancestral sequences
**3. Motif Discovery** - Extract consensus motifs - Identify binding sites - Characterize sequence patterns
1. **Pre-align sequences**: Ensure all sequences are properly aligned before consensus generation 2. **Quality sequences**: Use high-quality, verified sequences 3. **Consistent length**: All sequences must have identical lengths 4. **Consider gaps**: Decide how to handle gap characters 5. **Multiple alignments**: For large datasets, consider multiple consensus sequences