## 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]: domainsse.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