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dichet |
% dichet**************** EDIT HERE ****************
Mandatory qualifiers (* if not always prompted): [-inf] infile Name of raw input file (dictionary of heterogen groups) [-dogrep] boolean Search a directory of files with keywords? [-outf] outfile Name of output file * -path string Directory to search with keywords * -extn string Exension of files to search in above directory Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-inf] (Parameter 1) |
Name of raw input file (dictionary of heterogen groups) | Input file | Required |
[-dogrep] (Parameter 2) |
Search a directory of files with keywords? | Yes/No | No |
[-outf] (Parameter 3) |
Name of output file | Output file | <sequence>.dichet |
-path | Directory to search with keywords | Any string is accepted | ./ |
-extn | Exension of files to search in above directory | Any string is accepted | .ent |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
Program name | Description |
---|---|
contacts | Reads coordinate files and writes files of intra-chain residue-residue contact data |
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 |