![]() |
contactcount |
Standard (Mandatory) qualifiers: [-cmapdir] dirlist Directory of cleaned-chain contact files [-outfile] outfile File containing contact-based scoring matrix Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-cmapdir] (Parameter 1) |
Directory of cleaned-chain contact files | Directory with files | ./ |
[-outfile] (Parameter 2) |
File containing contact-based scoring matrix | Output file | <sequence>.contactcount |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
Under development, no example input file(s) yet
Under development, no example output file(s) yet
Program name | Description |
---|---|
contacts | Reads CCF files (clean coordinate files) and writes CON files (contact files) of intra-chain residue-residue contact data |
domainalign | Generates DAF files (domain alignment files) of structure-based sequence alignments for nodes in a DCF file (domain classification file) |
domainrep | Reorder DCF file (domain classification file) so that the representative structure of each user-specified node is given first |
domainreso | Removes low resolution domains from a DCF file (domain classification file) |
interface | Reads CCF files (clean coordinate files) and writes CON files (contact files) of inter-chain residue-residue contact data |
libgen | Generates various types of discriminating elements for each alignment in a directory |
psiphi | Calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file |
rocon | Reads a DHF file (domain hits file) of hits (sequences of unknown structural classification) and a DHF file of validation sequences (known classification) and writes a 'hits file' for the hits, which are classified and rank-ordered on the basis of score |
rocplot | Provides interpretation and graphical display of the performance of discriminating elements (e.g. profiles for protein families). rocplot reads file(s) of hits from discriminator-database search(es), performs ROC analysis on the hits, and writes graphs illustrating the diagnostic performance of the discriminating elements |
seqalign | Reads a DAF file (domain alignment file) and a DHF file (domain hits file) and writes a DAF file extended with the hits |
seqfraggle | Removes fragments from DHF files (domain hits files) or other files of sequences |
seqsearch | Generate database hits (sequences) for nodes in a DCF file (domain classification file) by using PSI-BLAST |
seqsort | Reads DHF files (domain hits files) of database hits (sequences) and removes hits of ambiguous classification |
seqwords | Generates DHF files (domain hits files) of database hits (sequences) for nodes in a DCF file (domain classification file) by keyword search of UniProt |
siggen | Generates a sparse protein signature from an alignment and residue contact data |
sigscan | Generates a DHF file (domain hits file) of hits (sequences) from scanning a signature against a sequence database |