| ## CATHPARSE 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

Generate DCF file from raw CATH files

## 2.0 INPUTS & OUTPUTS

CATHPARSE parses the CATH classification files, e.g. caths.list.v2.4, domlist.v2.4 and CAT.names.all.v2.4. These files are available by anonymous ftp from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4) The format of these files is explained in the README file available there. CATHPARSE writes the CATH classification to a DCF file (EMBL-like format). No changes are made to the data other than changing the format in which it is held. The input and output files are specified by the user.

## 3.0 INPUT FILE FORMAT

An excerpt from the raw CATH classification files, of the type caths.list.vX.X (Figure 1), domlist.vX.X (Figure 2) and CAT.names.all.vX.X (Figure 3) is shown below. The format of these files is explained in the CATH README file available by anonymous ftp from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4).

### Input files for usage example

### File: caths.list.small

    1cuk03    1  10   8  10   1   1   1  48 1.900
    1hjp03    1  10   8  10   1   1   2  44 2.500

### File: domlist.small

    1cuk00  D03   F00    1  0   1 - 0  66 -    1  0  67 - 0 142 -    1  0 156 - 0 203 -
    1hjp00 D03 F01  1  0    1 - 0   66 -  1  0   67 - 0  158 -  1  0  159 - 0  202 -  0  203 - 0  203 - (1)

### File: CAT.names.all.small

    1.10.8           1cuk03            :Helicase, Ruva Protein, domain 3
    1.10.8.10         1cuk03    :DNA helicase RuvA subunit, C-terminal domain
    0001             2ccyA0        :Mainly Alpha
    0001.0010        1eca00          :Orthogonal Bundle

## 4.0 OUTPUT FILE FORMAT

An example of the DCF output file is shown in Figure 4. The records used to describe an entry are as follows. Records (5) to (8) are used to describe the position of the domain in the CATH hierarchy.

- (1) ID - Domain identifier code. This is a 6-character code that uniquely identifies the domain in CATH. The first four characters are the PDB identifier code, the fifth character is the PDB chain identifier to which the domain belongs and the final character is the number of the domain in the chain (for chains comprising more than one domain). This character is '0' if the chain comprises a single domain only.
- (2) EN - PDB identifier code. This is the 4-character PDB identifier code of the PDB entry containing the domain.
- (3) TY - domain type. "CATH" or "SCOP" is given ("CATH" for DCF files generated by using CATHPARSE).
- (4) CI - CATH Classification Numbers. The integers preceeding the codes CL, AR, TP, SF, FA, NI, IF are the CATH classification numbers for CLass, ARchitecture, ToPology, Homologous SuPerfamily, FAmily, Near Identical family and Identical Family respectively. These numbers uniquely identify the appropriate node in the CATH parsable files.
- (5) CL - Class. It is the identical text taken from CAT.names.all.vX.X.
- (6) AR - Architecture. It is the identical text taken from CAT.names.all.vX.X.
- (7) TP - Topology. It is the identical text taken from CAT.names.all.vX.X.
- (8) SF - Homologous Superfamily. It is the identical text taken from CAT.names.all.vX.X.
- (9) DS - Sequence of the domain according to the PDB file. This sequence is taken from the domain CCF file (clean coordinate file) generated by DOMAINER. The DS record will only be present if the DCF file has been processed using DOMAINSEQS.
- (10) NR - Number of residues in domain
- (11) NC - Number of segments comprising the domain. All domains in CATH are from single chains. If the number of segments is greater than 1, then the domain entry will have a section containing a CN and a CH record (see below) for each segment.
- (12) CN - Segment number. The number given in brackets after this record indicates the start of the data for the relevent segment.
- (13) CH - Domain definition. The character given before CHAIN is the PDB chain identifier, the strings before START and END give the start and end positions respectively of the domain in the PDB file (a '.' is given in cases where a position was not specified). Note that the start and end positions refer to residue numbering given in the original pdb file and therefore must be treated as strings. (14) XX - used for spacing. (15) // - used to delimit records for a domain.

### Output files for usage example

### File: Ecath.dat

    ID   1CUK03
    XX
    EN   1CUK
    XX
    TY   CATH
    XX
    CI   1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;1 IF;
    XX
    CL   Mainly Alpha
    XX
    AR   Orthogonal Bundle
    XX
    TP   Helicase, Ruva Protein, domain 3
    XX
    SF   DNA helicase RuvA subunit, C-terminal domain
    XX
    NR   48
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   0 CHAIN; 156 START; 203 END;
    //
    ID   1HJP03
    XX
    EN   1HJP
    XX
    TY   CATH
    XX
    CI   1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;2 IF;
    XX
    CL   Mainly Alpha
    XX
    AR   Orthogonal Bundle
    XX
    TP   Helicase, Ruva Protein, domain 3
    XX
    SF   DNA helicase RuvA subunit, C-terminal domain
    XX
    NR   44
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   0 CHAIN; 159 START; 202 END;
    //

### File: cathparse.log

    1.10.8.10
    1.10.8
    0001.0010
    0001
    1.10.8.10
    1.10.8
    0001.0010
    0001

## 5.0 DATA FILES

None.

## 6.0 USAGE

### 6.1 COMMAND LINE ARGUMENTS

    Generate DCF file from raw CATH files.
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers:
      [-listfile]          infile     [caths.list.v2.4] This option specifies the
                                      name of raw CATH classification file
                                      (caths.list.vX.X) (input). The raw CATH
                                      parsable files (classification and
                                      description files) available from
                                      ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).
      [-domfile]           infile     [domlist.v2.4] This option specifies the
                                      name of raw CATH classification file
                                      (domlist.vX.X) (input). The raw CATH
                                      parsable files (classification and
                                      description files) available from
                                      ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).
      [-namesfile]         infile     [CAT.names.all.v2.4] This option specifies
                                      the name of raw CATH classification file
                                      (CAT.names.all.vX.X) (input). The raw CATH
                                      parsable files (classification and
                                      description files) available from
                                      ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).
      [-outfile]           outfile    [Ecath.dat] This option specifies the name
                                      of CATH DCF file (domain classification
                                      file) (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.
       -logfile            outfile    [cathparse.log] This option specifies the
                                      name of the CATHPARSE log file.

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

       "-outfile" associated qualifiers
       -odirectory4        string     Output directory

       "-logfile" associated qualifiers
       -odirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to 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 and exit. 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 dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-listfile] (Parameter 1) | infile | This option specifies the name of raw CATH classification file (caths.list.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). | Input file | caths.list.v2.4
[-domfile] (Parameter 2) | infile | This option specifies the name of raw CATH classification file (domlist.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). | Input file | domlist.v2.4
[-namesfile] (Parameter 3) | infile | This option specifies the name of raw CATH classification file (CAT.names.all.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). | Input file | CAT.names.all.v2.4
[-outfile] (Parameter 4) | outfile | This option specifies the name of CATH DCF file (domain classification file) (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 | Ecath.dat
-logfile | outfile | This option specifies the name of the CATHPARSE log file. | Output file | cathparse.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory4 -odirectory_outfile | string | Output directory | Any string |
"-logfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

### 6.2 EXAMPLE SESSION

An example of interactive use of CATHPARSE is shown below. Here is a sample session with cathparse

    % cathparse
    Generate DCF file from raw CATH files.
    Raw cath list file [caths.list.v2.4]: caths.list.small
    Raw cath domlist file [domlist.v2.4]: domlist.small
    Raw cath names file [CAT.names.all.v2.4]: CAT.names.all.small
    Domain classification output file [Ecath.dat]:
    Domainatrix log output file [cathparse.log]:

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

## 7.0 KNOWN BUGS & WARNINGS

## 8.0 NOTES

A future implementation will give the option of omitting from the output file domains that consist of more than one segment.
CATH includes several minor classes which are not appropriate for some anaylses. A future implementation will give the option to omit domains from minor classes.

### 8.1 GLOSSARY OF FILE TYPES

FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO
SCOP parsable files | CATH format. | Raw CATH classification data. | Available from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4) | N.A.
Domain classification file (for CATH) | DCF format (EMBL-like). | Classification and other data for domains from CATH. | CATHPARSE | Domain sequence information can be added to the file by using DOMAINSEQS.

## 9.0 DESCRIPTION

The raw CATH classification files are inconvenient for some uses because the text describing the domain classification is given in a different file to the classification itself, the file formats are not easily extended and differ from other related classifications such as SCOP. CATHPARSE reads the raw CATH classification files and writes a single file in DCF (EMBL-like) format, which is an easier format to work with, is more human-readable and is more extensible than the native CATH database format.

## 10.0 ALGORITHM

None.

## 11.0 RELATED APPLICATIONS

## See also

Program name | Description
--- | ---
aaindexextract | Extract amino acid property data from AAINDEX
allversusall | Sequence similarity data from all-versus-all comparison
cutgextract | Extract codon usage tables from CUTG database
domainalign | Generate alignments (DAF file) for nodes in a DCF file
domainer | Generate domain CCF files from protein CCF files
domainnr | Remove redundant domains from a DCF file
domainrep | Reorder DCF file to identify representative structures
domainseqs | Add sequence records to a DCF file
domainsse | Add secondary structure records to a DCF file
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
hetparse | Convert heterogen group dictionary to EMBL-like format
jaspextract | Extract data from JASPAR
libgen | Generate discriminating elements from alignments
matgen3d | Generate a 3D-1D scoring matrix from CCF files
pdbparse | Parse PDB files and writes protein CCF files
pdbplus | Add accessibility and secondary structure to a CCF file
pdbtosp | Convert swissprot:PDB codes file to EMBL-like format
pepcoil | Predict coiled coil regions in protein sequences
printsextract | Extract data from PRINTS database for use by pscan
prosextract | Process the PROSITE motif database for use by patmatmotifs
rebaseextract | Process the REBASE database for use by restriction enzyme applications
rocon | Generate a hits file from comparing two DHF files
rocplot | Perform ROC analysis on hits files
scopparse | Generate DCF file from raw SCOP files
seqalign | Extend alignments (DAF file) with sequences (DHF file)
seqfraggle | Remove fragment sequences from DHF files
seqnr | Remove redundancy from DHF files
seqsort | Remove ambiguous classified sequences from DHF files
seqwords | Generate DHF files from keyword search of UniProt
sites | Generate residue-ligand CON files from CCF files
ssematch | Search a DCF file for secondary structure matches
tfextract | Process TRANSFAC transcription factor database for use by tfscan

## 12.0 DIAGNOSTIC ERROR MESSAGES

None.

## 13.0 AUTHORS

Mike Hurley
Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK

## 14.0 REFERENCES

Please cite the authors and EMBOSS. Please cite the authors and EMBOSS.
Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

### 14.1 Other useful references

1. Conte, L.L., Ailey, B., Hubbard, T.J. Brenner, S.E., Murzin, A.G. and Chothia, C. (2000) SCOP: a structural classification of proteins database. Nucleic Acids Res. 28, 257-259.