If I want to apply the BlastP
-db_soft_mask flag using BLAST+ v 2.10.1, am I correct in thinking that I will need to build a masked database first (i.e. I can't apply the flag to a standard DB made using makeblastdb)? Also, this link says
Database masking has two modes. The first is known as "soft-masking", and BLAST uses the database mask only during the (initial) word-finding phase of BLAST. The second is known as "hard-masking", and BLAST uses the database mask during all phases of the search.
To clarify, does this mean that when a hit is found in the soft-masked database, the hit sequence is 'demasked' and analysed for HSPs in full?