| Program name | Description |
| helixturnhelix |
Identify nucleic acid-binding motifs in protein sequences
|
| pepcoil |
Predicts coiled coil regions in protein sequences
|
| cathparse |
Generates DCF file from raw CATH files
|
| domainnr |
Removes redundant domains from a DCF file
|
| domainseqs |
Adds 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
|
| domainalign |
Generate alignments (DAF file) for nodes in a DCF file
|
| domainrep |
Reorder DCF file to identify representative structures
|
| seqalign |
Extend alignments (DAF file) with sequences (DHF file)
|
| seqfraggle |
Removes fragment sequences from DHF files
|
| seqsort |
Remove ambiguous classified sequences from DHF files
|
| seqwords |
Generates DHF files from keyword search of UniProt
|
| libgen |
Generate discriminating elements from alignments
|
| matgen3d |
Generate a 3D-1D scoring matrix from CCF files
|
| rocon |
Generates a hits file from comparing two DHF files
|
| rocplot |
Performs ROC analysis on hits files
|