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masking algorithms
USEARCH provides several methods for masking. Query and database sequences can be masked independently using masking provided by an external program or one of the built-in masking algorithms.

Masking options

Option   Description
‑qmask method   Masking method for the query file. Used for database searches and clustering.
‑dbmask method   Masking method for the database. Used for makeudb_usearch and makeudb_ublast and when a database is loaded from a FASTA file. Ignored if the database is a UDB file; the desired masking must be applied when the UDB file is created.
-hardmask   Use hard masking (overwrite with N or X). Default is soft masking (upper case is unmasked, lower case is masked)..

Masking methods

Method Type Description
fastamino protein Unpublished method. Default for proteins.
fastnucleo nucleotide Unpublished method. Default for nucleotides.
seg protein Seg algorithm as used in BLASTP.
dust nucleotide Dust algorithm as used in BLASTN.
none both No masking, treat lower case and upper case letters as equivalent. This can be used if the input file has already been hard-masked.
user both Assume the input file has already been soft-masked so that lower case letters are masked.