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printsextract |
This program derives matrix information from the final motif sets of the PRINTS data file (prints.dat). It creates files in the EMBOSS data subdirectory PRINTS these being a matrix file and files containing text information for each fingerprint. Running this program may be the job of your system manager.
% printsextract Full pathname of PRINTS.DAT: /data/prints/prints.dat
Mandatory qualifiers: [-inf] infile Full pathname of prints.dat 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) |
Full pathname of prints.dat | Input file | Required |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
The PRINTS database is currently available via the anonymous ftp servers at:
It is also distributed on the EMBL CD-ROMs.
The home page for PRINTS is: http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
Program name | Description |
---|---|
aaindexextract | Extract data from AAINDEX |
cutgextract | Extract data from CUTG |
domainer | Reads protein coordinate files and writes domains coordinate files |
funky | Reads clean coordinate files and writes file of protein-heterogen contact data |
groups | Removes redundant hits from a scop families file |
hetparse | Converts raw dictionary of heterogen groups to a file in embl-like format |
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one |
pdbparse | Parses pdb files and writes cleaned-up protein coordinate files |
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scope | Convert raw scop classification file to embl-like format |
scopnr | Removes redundant domains from a scop classification file |
scopparse | Converts raw scop classification files to a file in embl-like format |
scopseqs | Adds pdb and swissprot sequence records to a scop classification file |
tfextract | Extract data from TRANSFAC |