| Program name | Description | 
|---|
| aaindexextract | Extract amino acid property data from AAINDEX | 
| cutgextract | Extract codon usage tables from CUTG database | 
| jaspextract | Extract data from JASPAR | 
| printsextract | Extract data from PRINTS database for use by pscan | 
| prosextract | Process the PROSITE motif database for use by patmatmotifs | 
| rebaseextract | Process the REBASE database for use by restriction enzyme applications | 
| tfextract | Process TRANSFAC transcription factor database for use by tfscan | 
| cathparse | Generate DCF file from raw CATH files | 
| domainnr | Remove redundant domains from a DCF file | 
| domainseqs | Add sequence records to a DCF file | 
| domainsse | Add secondary structure records to a DCF file | 
| scopparse | Generate DCF file from raw SCOP files | 
| ssematch | Search a DCF file for secondary structure matches | 
| allversusall | Sequence similarity data from all-versus-all comparison | 
| seqnr | Remove redundancy from DHF files | 
| domainer | Generate domain CCF files from protein CCF files | 
| hetparse | Convert heterogen group dictionary to EMBL-like format | 
| pdbparse | Parse PDB files and writes protein CCF files | 
| pdbplus | Add accessibility and secondary structure to a CCF file | 
| pdbtosp | Convert swissprot:PDB codes file to EMBL-like format | 
| sites | Generate residue-ligand CON files from CCF files |