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.
