QuestionsCategory: BIOSTARLocal vs. global alignment Staff asked 3 years ago

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

1 Answers Staff answered 3 years 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