When to use masking in BLAST?
When is it necessary to mask a database for BLAST?
For example, if I am going to be using queries that only contain coding sequences against a nucleotide database, to what extent will masking reduce false positives? Or is it mainly important for comparing non-coding regions? Or will it substantially reduce the time to search the database?
Thank you
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See this page for assistance with masking. Masking is mainly used for repetitive and low complexity sequences. I don't think masking will help with the use case you are describing.