Program name | Description |
contacts |
Reads coordinate files and writes files of intra-chain residue-residue contact data
|
dichet |
Parse dictionary of heterogen groups
|
hmmgen |
Generates a hidden Markov model for each alignment in a directory
|
interface |
Reads coordinate files and writes files of inter-chain residue-residue contact data
|
profgen |
Generates various profiles for each alignment in a directory
|
psiblasts |
Runs PSI-BLAST given scopalign alignments
|
scopalign |
Generate alignments for families in a scop classification file by using STAMP
|
scoprep |
Reorder scop classificaiton file so that the representative structure of each family is given first
|
scopreso |
Removes low resolution domains from a scop classification file
|
seqalign |
Generate extended alignments for families in a scop families file by using CLUSTALW with seed alignments
|
seqsearch |
Generate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments
|
seqsort |
Reads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus a validation file
|
seqwords |
Generate file of hits for scop families by searching swissprot with keywords
|
siggen |
Generates a sparse protein signature from an alignment and residue contact data
|
sigscan |
Scans a signature against swissprot and writes a signature hits files
|