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scope |
The SCOP database aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known, including all entries in the Protein Data Bank (PDB).
scope reads the SCOP classification file available at http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?dir=lin
scope writes the SCOP classification to an EMBL-like format file.
No changes are made to the data other than changing the format in which it is held.
This EMBL-like format SCOP file is used by several other EMBOSS programs.
The reason why the SCOP database format is changed to an EMBL-like format before being used used by other EMBOSS programs is that it is an easier format to work with than the native SCOP database format.
% scope Convert raw scop classification file to embl-like format Name of scop file for input (raw format) [scop.orig]: /data/scop/scop.orig Name of scop file for output (embl-like format) [Escop.dat]: Escop.test
Mandatory qualifiers: [-infile] infile Name of scop file for input (raw format) [-outfile] outfile Name of scop file for output (embl-like format) 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 | |
---|---|---|---|
[-infile] (Parameter 1) |
Name of scop file for input (raw format) | Input file | scop.orig |
[-outfile] (Parameter 2) |
Name of scop file for output (embl-like format) | Output file | Escop.dat |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
The format of this file is explained at http://scop.mrc-lmb.cam.ac.uk/scop/parindex.html
The file given at this URL contains a single line for each domain in SCOP, including text describing the position of the domain in the SCOP hierarchy. Note that other SCOP classification files, without this annotation, are available at http://scop.mrc-lmb.cam.ac.uk/scop/parindex.html
An example of an excerpt from an output file follows:
ID D3SDHA_ XX EN 3SDH XX OS Ark clam (Scapharca inaequivalvis) XX CL All alpha proteins XX FO Globin-like XX SF Globin-like XX FA Globins XX DO Hemoglobin I XX NC 1 XX CN [1] XX CH a CHAIN; . START; . END; // ID D3SDHB_ XX EN 3SDH XX OS Ark clam (Scapharca inaequivalvis) XX CL All alpha proteins XX FO Globin-like XX SF Globin-like XX FA Globins XX DO Hemoglobin I XX NC 1 XX CN [1] XX CH b CHAIN; . START; . END; //
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 |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
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 |