
DOMAINSSE documentation

CONTENTS

   1.0 SUMMARY 
   2.0 INPUTS & OUTPUTS 
   3.0 INPUT FILE FORMAT 
   4.0 OUTPUT FILE FORMAT 
   5.0 DATA FILES 
   6.0 USAGE 
   7.0 KNOWN BUGS & WARNINGS 
   8.0 NOTES 
   9.0 DESCRIPTION 
   10.0 ALGORITHM 
   11.0 RELATED APPLICATIONS 
   12.0 DIAGNOSTIC ERROR MESSAGES 
   13.0 AUTHORS 
   14.0 REFERENCES 

1.0 SUMMARY

   Adds secondary structure records to a DCF file (domain classification
   file)

2.0 INPUTS & OUTPUTS

   DOMAINSSE parses a DCF file (domain classification file) and writes a
   file containing the same data, except that domain secondary structure
   information derived from structural are added. Domain sequences are
   taken from domain CCF files (clean coordinate files). The CCF files
   must contain secondary structure information, which can be added by
   using PDBPLUS. The path for the CCF files (input) and names of DCF
   files (input and output) are specified by the user. The extension of
   CCF files is specified in the ACD file. A log file is also written.

3.0 INPUT FILE FORMAT

   The format of the DCF file is described in the SCOPPARSE
   documentation.

  Input files for usage example

  File: all.scop

ID   D1CS4A_
XX
EN   1CS4
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Adenylyl cyclase VC1, domain C1a
XX
OS   Dog (Canis familiaris)
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

4.0 OUTPUT FILE FORMAT

   The format of the DCF file is described in the SCOPPARSE
   documentation. DOMAINRESO adds the following records:
     * (1) SS - Secondary structure assignment (per residue). A
       simplified 3-state assignment: H (helix), E (extended, beta
       strand) and L (loop, open coil) is used.
     * (2) SE - Secondary structure element assignment (per secondary
       structure element). The same 3-state assignment as for the SS
       record is used: H (helix), E (extended, beta strand) and L (loop,
       open coil).

  Output files for usage example

  File: domainsse.out

ID   D1CS4A_
XX
EN   1CS4
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Adenylyl cyclase VC1, domain C1a
XX
OS   Dog (Canis familiaris)
XX
SE   EEEEEEE
XX
SS   SEQUENCE   189 AA;  24290 MW;  D1929097 CRC32;
     LLLLLLLEEE EEEEEEEEEE ELHHHHHHHL LHHHHHHHHH HHHHHHHHHH HHHHLLEEEE
     EELLEEEEEE LLLLLLLHHH HHHHHHHHHH HHHHHHHHHH HHLLLLEEEE EEEEEEEEEL
     LLLLLLLLEE EHHHHHHHHH HHHHLLLLLE EEEHHHHHLL LLLLLEEELH HHHHHHHHHH
     HLLLEEEEL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
SE   HEEE
XX
SS   SEQUENCE    43 AA;   5411 MW;  61C5458D CRC32;
     LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

  File: DOMAINSSE.log

5.0 DATA FILES

   None.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers:
  [-dcfinfile]         infile     This option specifies the name of the DCF
                                  file (domain classification file) (input). A
                                  'domain classification file' contains
                                  classification and other data for domains
                                  from SCOP or CATH, in DCF format
                                  (EMBL-like). The files are generated by
                                  using SCOPPARSE and CATHPARSE. Domain
                                  sequence information can be added to the
                                  file by using DOMAINSEQS.
  [-dccfdir]           directory  This option specifies the location of the
                                  domain CCF file (clean coordinate files)
                                  (input). A 'clean cordinate file' contains
                                  protein coordinate and derived data for a
                                  single PDB file ('protein clean coordinate
                                  file') or a single domain from SCOP or CATH
                                  ('domain clean coordinate file'), in CCF
                                  format (EMBL-like). The files, generated by
                                  using PDBPARSE (PDB files) or DOMAINER
                                  (domains), contain 'cleaned-up' data that is
                                  self-consistent and error-corrected.
                                  Records for residue solvent accessibility
                                  and secondary structure are added to the
                                  file by using PDBPLUS.
  [-dcfoutfile]        outfile    This option specifies the name of the DCF
                                  file (domain classification file) with
                                  secondary structure records (output). A
                                  'domain classification file' contains
                                  classification and other data for domains
                                  from SCOP or CATH, in DCF format
                                  (EMBL-like). The files are generated by
                                  using SCOPPARSE and CATHPARSE. Domain
                                  sequence information can be added to the
                                  file by using DOMAINSEQS.
  [-errfile]           outfile    This option specifies the name of the
                                  DOMAINSSE log file.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-dcfoutfile" associated qualifiers
   -odirectory3        string     Output directory

   "-errfile" associated qualifiers
   -odirectory4        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
   [-dcfinfile]
   (Parameter 1) This option specifies the name of the DCF file (domain
   classification file) (input). A 'domain classification file' contains
   classification and other data for domains from SCOP or CATH, in DCF
   format (EMBL-like). The files are generated by using SCOPPARSE and
   CATHPARSE. Domain sequence information can be added to the file by
   using DOMAINSEQS. Input file Required
   [-dccfdir]
   (Parameter 2) This option specifies the location of the domain CCF
   file (clean coordinate files) (input). A 'clean cordinate file'
   contains protein coordinate and derived data for a single PDB file
   ('protein clean coordinate file') or a single domain from SCOP or CATH
   ('domain clean coordinate file'), in CCF format (EMBL-like). The
   files, generated by using PDBPARSE (PDB files) or DOMAINER (domains),
   contain 'cleaned-up' data that is self-consistent and error-corrected.
   Records for residue solvent accessibility and secondary structure are
   added to the file by using PDBPLUS. Directory ./
   [-dcfoutfile]
   (Parameter 3) This option specifies the name of the DCF file (domain
   classification file) with secondary structure records (output). A
   'domain classification file' contains classification and other data
   for domains from SCOP or CATH, in DCF format (EMBL-like). The files
   are generated by using SCOPPARSE and CATHPARSE. Domain sequence
   information can be added to the file by using DOMAINSEQS. Output file
   <sequence>.domainsse
   [-errfile]
   (Parameter 4) This option specifies the name of the DOMAINSSE log
   file. Output file DOMAINSSE.log
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

  6.2 EXAMPLE SESSION

   An example of interactive use of DOMAINSSE is shown below. Here is a
   sample session with domainsse


% domainsse 
Adds secondary structure records to a DCF file (domain classification
file).
Name of DCF file (domain classification file) (input): all.scop
Location of domain CCF file (clean coordinate file) (input) [./]: 
Name of DCF file (domain classification file) (output) [all.domainsse]: domains
se.out
Name of DOMAINSSE log file. [DOMAINSSE.log]: DOMAINSSE.log

Processing D1CS4A_
Processing D1II7A_

Done!
 output file name: domainsse.out
 log file name: DOMAINSSE.log

   Go to the input files for this example
   Go to the output files for this example

   The DCF file (domain classification file) lacking secondary structure
   information called /test_data/all.scop was parsed and a DCF file with
   secondary structure information called
   /test_data/domainseqs/all_s.scop was written. Secondary structure
   information was taken from CCF files in test_data/. A log file called
   /test_data/domainseqs/DOMAINSSE.log was written.

7.0 KNOWN BUGS & WARNINGS

   None.

8.0 NOTES

  8.1 GLOSSARY OF FILE TYPES

   FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
   Domain classification file (for SCOP) DCF format (EMBL-like format for
   domain classification data). Classification and other data for domains
   from SCOP. SCOPPARSE Domain sequence information can be added to the
   file by using DOMAINSEQS.
   Domain classification file (for CATH) DCF format (EMBL-like format for
   domain classification data). Classification and other data for domains
   from CATH. CATHPARSE Domain sequence information can be added to the
   file by using DOMAINSEQS.
   Clean coordinate file (for protein) CCF format (EMBL-like format for
   protein coordinate and derived data). Coordinate and other data for a
   single PDB file. The data are 'cleaned-up': self-consistent and
   error-corrected. PDBPARSE Records for residue solvent accessibility
   and secondary structure are added to the file by using PDBPLUS.
   Clean coordinate file (for domain) CCF format (EMBL-like format for
   protein coordinate and derived data). Coordinate and other data for a
   single domain from SCOP or CATH. The data are 'cleaned-up':
   self-consistent and error-corrected. DOMAINER Records for residue
   solvent accessibility and secondary structure are added to the file by
   using PDBPLUS.

   None

9.0 DESCRIPTION

   Domain secondary structure information is not given in the raw SCOP or
   CATH parsable files, but is required for many analyses and for
   convenience should, ideally, be provided along with the classification
   itself. DOMAINSSE reads a DCF file (domain classificaiton file) that
   lacks secondary structure information and writes one containing such
   information.

10.0 ALGORITHM

   None.

11.0 RELATED APPLICATIONS

See also

   Program name Description
   aaindexextract Extract data from AAINDEX
   allversusall Does an all-versus-all global alignment for each set of
   sequences in an input directory and writes files of sequence
   similarity values
   cathparse Reads raw CATH classification files and writes DCF file
   (domain classification file)
   cutgextract Extract data from CUTG
   domainer Reads CCF files (clean coordinate files) for proteins and
   writes CCF files for domains, taken from a DCF file (domain
   classification file)
   domainnr Removes redundant domains from a DCF file (domain
   classification file). The file must contain domain sequence
   information, which can be added by using DOMAINSEQS
   domainseqs Adds sequence records to a DCF file (domain classification
   file)
   hetparse Converts raw dictionary of heterogen groups to a file in
   EMBL-like format
   pdbparse Parses PDB files and writes CCF files (clean coordinate
   files) for proteins
   pdbplus Add residue solvent accessibility and secondary structure data
   to a CCF file (clean coordinate file) for a protein or domain
   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
   scopparse Reads raw SCOP classification files and writes a DCF file
   (domain classification file)
   seqnr Removes redundancy from DHF files (domain hits files) or other
   files of sequences
   sites Reads CCF files (clean coordinate files) and writes CON files
   (contact files) of residue-ligand contact data for domains in a DCF
   file (domain classification file)
   ssematch Searches a DCF file (domain classification file) for
   secondary structure matches
   tfextract Extract data from TRANSFAC

12.0 DIAGNOSTIC ERROR MESSAGES

   None.

13.0 AUTHORS

   Jon Ison (jison@rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

14.0 REFERENCES

   Please cite the authors and EMBOSS.
   Rice P, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology
   Open Software Suite. Trends in Genetics, 15:276-278. See also
   http://www.uk.embnet.org/Software/EMBOSS

  14.1 Other useful references
