QuestionsCategory: BIOSTARLocal vs. global alignment Staff asked 10 months ago

How do we decide if we should use local or global alignment?

1 Answers Staff answered 10 months ago

It depends on your input sequences. Local alignments are useful for finding regions of similarity between dissimilar sequences. Global alignments do more of an end-to-end alignment between two sequences. If you have two very dissimilar sequences you’ll probably get a lot of gaps between your two sequences when you do a global alignment. A local alignment might be good for finding similar domains in two unrelated proteins; or maybe trying to find a transcription factor binding site in two promoter sequences. – answered by Des Tillo