- predicting the three-dimensional structure of a protein sequence: An alignment to an existing sequence with a known structure can hint at possible motifs in the new sequence, which allows secondary structures to be predicted more easily (and by extension higher-order structures).
- introducing random mutations into a protein sequence for the purposes of a directed (in vitro) evolution experiment: The mutations introduced could be selective. A researcher could run tests of mutations on conserved motifs (regions with good alignment) to note the importance of the motif, or mutate regions with bad alignment to "fine-tune" the sequence.
- determining whether a particular bacterial gene has been introduced to its host genome via a "horizontal transfer" event: The modified host genome could be aligned to the region around the bacterial gene to see if the sequences align; if they do, and there is a significant difference from the alignment vs. an alignment made on a control, then it is very likely that a horizontal gene transfer event occurred.
- attempting to identify regulatory elements (such as riboswitches) in a genome sequence: Alignments of complementary sequences of known regulatory binding elements could be made to the sequence of interest, and regions with high alignment are likely to be binding sites for the regulatory binding elements.
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