USEARCH manual > options > default index parameters
default index parameters
 
Default values of index parameters are determined from the command name and sequence type (nucleotide or protein). UBLAST parameters apply to the ublast command, USEARCH parameters apply to usearch_ and cluster_ commands.
 
Parameter UBLAST
 protein		 USEARCH
 protein		 UBLAST
 nucleotide		 USEARCH
 nucleotide
-wordlength (use pattern) 5 8 8
-pattern 10111011 (use kmers) (use kmers) (use kmers)
-alpha (see below) aa nt nt
‑dbstep 1 1 1 1
-dbaccel 1.0 1.0 1.0 1.0
‑slots (don't hash) (don't hash) (don't hash) (don't hash)

 The default alphabet for protein ublast is A,KR,DENQ,C,G,H,ILVM,FYW,P,ST.