| Program name | Description | 
|---|
| antigenic | Finds antigenic sites in proteins | 
| digest | Protein proteolytic enzyme or reagent cleavage digest | 
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites | 
| fuzzpro | Protein pattern search | 
| fuzztran | Protein pattern search after translation | 
| helixturnhelix | Report nucleic acid binding motifs | 
| oddcomp | Find protein sequence regions with a biased composition | 
| patmatdb | Search a protein sequence with a motif | 
| patmatmotifs | Search a PROSITE motif database with a protein sequence | 
| pepcoil | Predicts coiled coil regions | 
| preg | Regular expression search of a protein sequence | 
| pscan | Scans proteins using PRINTS | 
| sigcleave | Reports protein signal cleavage sites | 
| omeme | Motif detection | 
| emast | Motif detection | 
| ememe | Motif detection |