Entering edit mode
4.6 years ago
DNAlias
▴
40
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
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.