| ## 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

Adds sequence records to a DCF file (domain classification 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.

## 4.0 OUTPUT FILE FORMAT

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

## 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

       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     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    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.
       -errfile            outfile    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    This option specifies the residue
                                      substitution matrix, which is used for
                                      sequence comparison.
    *  -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.
    *  -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. An exception is where one or
                                      both sequences are single reads with
                                      possible sequencing errors in which case you
                                      would expect many single base gaps. You can
                                      get this result by setting the gap open
                                      penalty to zero (or very low) and using the
                                      gap extension penalty to control gap
                                      scoring.

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

       "-dcfoutfile" associated qualifiers
       -odirectory3        string     Output directory

       "-errfile" associated qualifiers
       -odirectory         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 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) | 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 | Retrieve swissprot sequence. | Toggle value Yes/No | No
-pdbtospfile | 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) | 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
-errfile | 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 | Allowed values | Default
-datafile | This option specifies the residue substitution matrix, which is used for sequence comparison. | Comparison matrix file in EMBOSS data path | EBLOSUM62
-gapopen | 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 | 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. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

### 6.2 EXAMPLE SESSION

An example of interactive use of DOMAINSEQS is shown below.
The DCF file (domain classification file) lacking sequence information called /test_data/all.scop was parsed and a DCF file with sequence information called /test_data/domainseqs/all_s.scop was written. The file Epdbtosp.dat was queried for accession numbers of PDB files corresponding to the domains in all.scop, but no accession numbers were found for either of the domains d1ii7a_ or d1cs4a_. A log file called /test_data/domainseqs/domainseqs.log was written.

## 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

** The swissprot:PDB equivalence file is generated by pdbtosp and is part of ** the emboss distribution.

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 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
domainsse | Adds secondary structure 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

Ranjeeva Ranasinghe (rranasin@hgmp.mrc.ac.uk)
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, 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