| Program name | Description |
| profit |
Scan one or more sequences with a simple frequency matrix
|
| prophecy |
Create frequency matrix or profile from a multiple alignment
|
| prophet |
Scan one or more sequences with a Gribskov or Henikoff profile
|
| seqsearch |
Generate PSI-BLAST hits (DHF file) from a DAF file
|
| siggen |
Generate a sparse protein signature from an alignment
|
| siggenlig |
Generate ligand-binding signatures from a CON file
|
| sigscan |
Generate hits (DHF file) from a signature search
|
| sigscanlig |
Search ligand-signature library and writes hits (LHF file)
|