| ## DOMAINSEQS 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

Add sequence records to a DCF file

## 2.0 INPUTS & OUTPUTS

DOMAINSEQS parses a DCF file (domain classification file) and writes a file containing the same data, except that domain sequence information derived from structural and, optionally, sequence databases are added. Domain sequences are taken from domain CCF files (clean coordinate files) and (optionally) the swissprot database. If the swissprot sequence is used, DOMAINSEQS requires a swissprot:PDB equivalence file that gives the accession number of each PDB file corresponding to the domains in the DCF file. The path for the CCF files (input) and names of DCF files (input and output) are specified by the user. 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: ../scopparse-keep/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;
    //

### File: ../pdbtosp-domainatrix/Epdbtosp.dat

    EN   101M
    XX
    NE   1
    XX
    IN   MYG_PHYCA ID; P02185 ACC;
    XX
    //
    EN   102L
    XX
    NE   1
    XX
    IN   LYCV_BPT4 ID; P00720 ACC;
    XX
    //
    EN   102M
    XX
    NE   1
    XX
    IN   MYG_PHYCA ID; P02185 ACC;
    XX
    //
    EN   103L
    XX
    NE   1
    XX
    IN   LYCV_BPT4 ID; P00720 ACC;
    XX
    //
    EN   103M
    XX
    NE   1
    XX
    IN   MYG_PHYCA ID; P02185 ACC;
    XX
    //
    EN   9XIA
    XX
    NE   1
    XX
    IN   XYLA_STRRU ID; P24300 ACC;
    XX
    //
    EN   9XIM
    XX
    NE   1
    XX
    IN   XYLA_ACTMI ID; P12851 ACC;
    XX
    //

## 4.0 OUTPUT FILE FORMAT

The format of the DCF file is described in the SCOPPARSE documentation.
DOMAINSEQS may add the following records:

- (1) AC - Accession number of the domain sequence. This record will only be present if the DCF file has been processed using DOMAINSEQS and if an accession number for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of.
- (2) SP - Swissprot code of the domain sequence. This record will only be present if the domain classification file has been processed using DOMAINSEQS and if an swissprot code for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of.
- (3) RA - Position of domain in swissprot sequence. The integers preceeding START and END give the start and end points respectively of the domain sequence relative to the full-length swissprot sequence.
- (4) SQ - Sequence of the domain according to swissprot. This sequence is taken from the swissprot database. The SQ record will only be present if the SCOP classification file has been processed using DOMAINSEQS and if an accession number for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of.

### Output files for usage example

### File: all_s.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
    DS   SEQUENCE    52 AA;   5817 MW;  D8CCAE0E1FC0849A CRC64;
         ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
    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
    DS   SEQUENCE    65 AA;   7395 MW;  75FBE75B22FD3678 CRC64;
         MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
         LKKAI
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   A CHAIN; . START; . END;
    //

### File: domainseqs.log

    //
    D1CS4A_
    NO_ACCESSION_NUMBER
    //
    D1II7A_
    NO_ACCESSION_NUMBER

## 5.0 DATA FILES

If the user specified retrieval of sequences from a sequence database, DOMAINSEQS uses a swissprot:PDB equivalence file is generated by using PDBTOSP.

## 6.0 USAGE

### 6.1 COMMAND LINE ARGUMENTS

    Add sequence records to a DCF file.
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers (* if not always prompted):
      [-dcfinfile]         infile     This option specifies the name of 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.
      [-dpdbdir]           directory  [./] This option specifies the location of
                                      domain CCF file (clean coordinate files)
                                      (input). A 'clean cordinate file' contains
                                      coordinate and other data for a single PDB
                                      file or a single domain from SCOP or CATH,
                                      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.
       -getswiss           toggle     [N] Retrieve swissprot sequence.
    *  -pdbtospfile        infile     This option specifies the name of the
                                      pdbcodes to swissprot indexing file. The
                                      swissprot:PDB equivalence file is generated
                                      by PDBTOSP
      [-dcfoutfile]        outfile    [domainseqs.out] This option specifies the
                                      name of 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    [domainseqs.log] This option specifies the
                                      name of log file for the build. The log file
                                      contains messages about any errors arising
                                      while domainseqs ran.

       Additional (Optional) qualifiers (* if not always prompted):
    *  -datafile           matrixf    [EBLOSUM62] This option specifies the
                                      residue substitution matrix, which is used
                                      for sequence comparison.
    *  -gapopen            float      [10.0 for any sequence] This option
                                      specifies the gap insertion penalty. This is
                                      the score taken away when a gap is created.
                                      The best value depends on the choice of
                                      comparison matrix. The default value assumes
                                      you are using the EBLOSUM62 matrix for
                                      protein sequences, and the EDNAFULL matrix
                                      for nucleotide sequences. (Floating point
                                      number from 1.0 to 100.0)
    *  -gapextend          float      [0.5 for any sequence] This option specifies
                                      the gap extension penalty. This is added to
                                      the standard gap penalty for each base or
                                      residue in the gap. This is how long gaps
                                      are penalized. Usually you will expect a few
                                      long gaps rather than many short gaps, so
                                      the gap extension penalty should be lower
                                      than the gap penalty. (Floating point number
                                      from 0.0 to 10.0)

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

       "-dpdbdir" associated qualifiers
       -extension2         string     Default file extension

       "-dcfoutfile" associated qualifiers
       -odirectory3        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
[-dcfinfile] (Parameter 1) | infile | This option specifies the name of 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
[-dpdbdir] (Parameter 2) | directory | This option specifies the location of domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, 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 | ./
-getswiss | toggle | Retrieve swissprot sequence. | Toggle value Yes/No | No
-pdbtospfile | infile | This option specifies the name of the pdbcodes to swissprot indexing file. The swissprot:PDB equivalence file is generated by PDBTOSP | Input file | Required
[-dcfoutfile] (Parameter 3) | outfile | This option specifies the name of 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 | domainseqs.out
-logfile | outfile | This option specifies the name of log file for the build. The log file contains messages about any errors arising while domainseqs ran. | Output file | domainseqs.log
Additional (Optional) qualifiers
-datafile | matrixf | This option specifies the residue substitution matrix, which is used for sequence comparison. | Comparison matrix file in EMBOSS data path | EBLOSUM62
-gapopen | float | This option specifies the gap insertion penalty. This is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence
-gapextend | float | This option specifies the gap extension penalty. This is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-dpdbdir" associated directory qualifiers
-extension2 -extension_dpdbdir | string | Default file extension | Any string | ccf
"-dcfoutfile" associated outfile qualifiers
-odirectory3 -odirectory_dcfoutfile | 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 DOMAINSEQS is shown below. Here is a sample session with domainseqs

    % domainseqs
    Add sequence records to a DCF file.
    Domain classification file: ../scopparse-keep/all.scop
    Clean domain coordinates directory [./]: ../domainer-domainatrix
    Retrieve swissprot sequence. [N]: Y
    Swissprot:pdb equivalence table file (optional): ../pdbtosp-domainatrix/Epdbtosp.dat
    Domain classification output file [domainseqs.out]: all_s.scop
    Domainatrix log output file [domainseqs.log]:

    //
    D1CS4A_
    //
    D1II7A_

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

## 7.0 KNOWN BUGS & WARNINGS

The swissprot:PDB equivalence file available as part of the EMBOSS distribution does not contain accession numbers for all PDB files and covers only a relatively small proportion of domains in SCOP.

## 8.0 NOTES

DOMAINSEQS will not attempt to retrieve a swissprot sequence for any domains comprised of more than a single segment, i.e. for domains whose NC record in the DCF file has a value other than 1 (see SCOPPARSE documentation).
The region of sequence to retrieve is identified by alignment of the sequence from the CCF file (structural database) to the full length sequences in swissprot. If this were to be done for segmented domains, the start and end point for the retrieved sequence (relative to the full length sequence) might actually include a completely different domain.
Consider :
(A) represents a sequence from the coordinate file for a segmented domain D1
(B) represents the full-length swissprot sequence, it includes D1, but D1 is split by a second domain D2

                     D1
      (A)  XXXXXXXXXXXXXXXXXXXXX

              D1         D2        D1
      (B) XXXXXXXXXX-----------XXXXXXXXXXX

It should be clear that for an alignment retrieving B, the start and end points for the retrieved sequence would be misleading.
The user should be aware that sequences from the domain CCF file for domains comprised of more than a single segment are not biologically significant, as the sequences are derived from different segments of one or more chains. However, such sequences might be acceptable for redundancy calculations (e.g. by using DOMAINNR) because two redundant domains made of similar fragments will have similar sequences, so the redundancy should be detectable.

### 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.
swissprot:PDB equivalence file | EMBL-like format. | A file containing swissprot identifiers for PDB codes. | Included in the EMBOSS distribution | N.A.

None

## 9.0 DESCRIPTION

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

## 10.0 ALGORITHM

In order to find the start and end of a domain in a sequence from swissprot, the domain sequence from the domain CCF file is aligned to the full length protein sequence from swissprot. Alignment is performed first by string handling and if that fails, by using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. Gap insertion and extension penalties used in the alignments are user-specified.

## 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
cathparse | Generate DCF file from raw CATH files
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
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

Ranjeeva Ranasinghe
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.
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