Sequence Alignment
Sequence alignment is fundamental to comparative analysis in molecular biology. AI Scientist supports three alignment modes, from simple pairwise comparisons to large-scale database searches, all accessible directly within your research conversation.
Pairwise Alignment
Section titled “Pairwise Alignment”Compare two sequences side by side to identify regions of similarity, mismatches, and gaps. Pairwise alignment is commonly used to:
- Verify that a cloned construct matches the intended design
- Compare a wild-type sequence with a mutant variant to confirm introduced changes
- Assess sequence identity between homologs from different organisms
Results include an alignment visualization with color-coded matches/mismatches, identity and similarity percentages, and gap statistics.
Multiple Sequence Alignment (MSA)
Section titled “Multiple Sequence Alignment (MSA)”Align three or more sequences simultaneously to identify conserved regions and variable positions across a set of related sequences. MSA is essential for:
- Identifying conserved functional domains across protein families
- Guiding mutagenesis by highlighting positions that tolerate variation
- Constructing phylogenetic relationships between homologous sequences
AI Scientist renders MSA results as an interactive alignment viewer with conservation scoring and consensus sequence display.
BLAST Search
Section titled “BLAST Search”Search the NCBI public databases using BLAST (Basic Local Alignment Search Tool) to find sequences similar to your query. BLAST search is useful for:
- Identifying homologs of your gene of interest in other organisms
- Verifying sequence identity against reference databases
- Discovering related sequences for comparative studies or primer design
Results include top hits with alignment scores, E-values, percent identity, and direct links to the source database entries.