EMBOSS: nrscope

| ## EMBOSS: nrscope

# Program nrscope

## Function

Converts redundant EMBL-format SCOP file to non-redundant one

## Description

Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. A knowledge of these relationships is crucial to our understanding of the evolution of proteins and of development. It will also play an important role in the analysis of the sequence data that is being produced by worldwide genome projects.

The SCOP database aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known, including all entries in the Protein Data Bank (PDB).

nrscope reads in the EMBL-like format SCOP classification file generated by the EMBOSS application scope, and writes a file of non-redundant domains in the same format. Domain sequences are extracted from the clean domain coordinate files generated by the EMBOSS application domainer.

The current version of nrscope removes redundancy at the level of the SCOP family, i.e. entries belonging to the same family will be non-redundant. All permutations of pair-wise sequence alignments are calculated for each SCOP family in turn, using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. If a pair of proteins achieve greater than a threshold percentage sequence identity (specified by the user) the shortest sequence is discarded. The user must specify gap insertion and extension penalties and a residue substitution matrix for use in the alignments.

## Usage

Here is a sample session with nrscope:

    % nrscope
    Converts redundant EMBL-format SCOP file to non-redundant one
    Name of scop file for input (embl-like format) [Escop.dat]: /data/scop/Escop.dat
    Name of non-redundant scop file for output (embl-like format) [EscopNR.dat]: EscopNR.test
    Location of clean domain coordinate files for input (embl-like format) [./]: /data/cpdbscop/
    File extension of clean domain coordinate files [.pxyz]:
    The % sequence identity redundancy threshold [95]: 95
    Residue substitution file [EBLOSUM62]:
    Gap insertion penalty [10]: 20
    Gap extension penalty [0.5]: 1
    Name of log file for the build [nrscope.log]: EscopNR.log
    D3SDHA_
    D3SDHB_
    D3HBIA_
    D3HBIB_
    D4SDHA_
    D4SDHB_
    D4HBIA_
    D4HBIB_
    D5HBIA_
    D5HBIB_

## Command line arguments

       Mandatory qualifiers:
      [-scopin]            infile     Name of scop file for input (embl-like
                                      format)
      [-dpdb]              string     Location of clean domain coordinate files
                                      for input (embl-like format)
      [-extn]              string     File extension of clean domain coordinate
                                      files
      [-thresh]            float      The % sequence identity redundancy threshold
      [-datafile]          matrixf    Residue substitution matrix
      [-gapopen]           float      The gap insertion penalty 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      The gap extension, penalty 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.
      [-scopout]           outfile    Name of non-redundant scop file for output
                                      (embl-like format)
      [-errf]              outfile    Name of log file for the build

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-scopin] (Parameter 1) | Name of scop file for input (embl-like format) | Input file | Escop.dat
[-dpdb] (Parameter 2) | Location of clean domain coordinate files for input (embl-like format) | Any string is accepted | ./
[-extn] (Parameter 3) | File extension of clean domain coordinate files | Any string is accepted | .pxyz
[-thresh] (Parameter 4) | The % sequence identity redundancy threshold | Any integer value | 95.0
[-datafile] (Parameter 5) | Residue substitution matrix | Comparison matrix file in EMBOSS data path | EBLOSUM62
[-gapopen] (Parameter 6) | The gap insertion penalty 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] (Parameter 7) | The gap extension, penalty 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
[-scopout] (Parameter 8) | Name of non-redundant scop file for output (embl-like format) | Output file | EscopNR.dat
[-errf] (Parameter 9) | Name of log file for the build | Output file | nrscope.log
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

The EMBL-like format SCOP classification file generated by the EMBOSS application scope is as follows:

Records (4) to (8) are used to describe the position of the domain in the scop hierarchy.

1. ID - Domain identifier code. This is a 7-character code that uniquely identifies the domain in scop. It is identical to the first 7 characters of a line in the scop classification file. The first character is always 'D', the next four characters are the PDB identifier code, the fifth character is the PDB chain identifier to which the domain belongs (a '.' is given in cases where the domain is composed of multiple chains, a '_' is given where a chain identifier was not specified in the PDB file) and the final character is the number of the domain in the chain (for chains comprising more than one domain) or '_' (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. OS - Source of the protein. It is identical to the text given after 'Species' in the scop classification file.
4. CL - Domain class. It is identical to the text given after 'Class' in the scop classification file.
5. FO - Domain fold. It is identical to the text given after 'Fold' in the scop classification file.
6. SF - Domain superfamily. It is identical to the text given after 'Superfamily' in the scop classification file.
7. FA - Domain family. It is identical to the text given after 'Family' in the scop classification file.
8. DO - Domain name. It is identical to the text given after 'Protein' in the scop classification file.
9. NC - Number of chains comprising the domain (usually 1). If the number of chains is greater than 1, then the domain entry will have a section containing a CN and a CH record (see below) for each chain.
10. CN - Chain number. The number given in brackets after this record indicates the start of the data for the relevent chain.
11. CH - Domain definition. The character given before CHAIN is the PDB chain identifier (a '.' is given in cases where a chain identifier was not specified in the scop classification file), 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.

## Output file format

The output file has the same format as the input EMBL-like format SCOP classification file generated by the EMBOSS application scope except that it contains non-redundant domains, as explained in the Description section.

nrscope generates a log file, an excerpt of which is shown below. The first two lines describe the level in the SCOP hierarchy at which redundancy was removed (always 'FAMILIES' for the current implementation) and the value of the redundancy threshold. The file then contains a section for each SCOP family. Each section contains a line with the record '//' immediately followed by the name of the SCOP family, and two lines containing 'Retained' and 'Rejected' respectively. Domain identifier codes of domains that were discarded by nrscope are listed under 'Rejected' while those that appear in the output file are listed under 'Retained'. The text 'WARN filename not found' is given in cases where a clean domain coordinate file could not be found and 'WARN Empty family' where no files for an entire family could be found. 'ERROR filename file read error' will be given when an error was encountered during a file read.

    FAMILIES are non-redundant
    95% redundancy threshold
    // Homeodomain
    Retained
    D2HDDA_
    D1AKHA_
    D1MNMC_
    Rejected
    D2HDDB_
    D1ENH__
    D3HDDA_
    WARN  d3hdda_.pxyz not found
    // Di-haem cytohrome c peroxidase
    WARN  ds005__.pxyz not found
    WARN  Empty family
    // Nuclear receptor coactivator Src-1
    Retained
    D2PRGC_
    Rejected

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
cutgextract | Extract data from CUTG
domainer | Build domain coordinate files
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
scope | Convert raw scop classification file to embl-like format
scopparse | Reads raw scop classifications file and writes embl-like format scop classification file
seqnr | Converts redundant database results to a non-redundant set of hits
tfextract | Extract data from TRANSFAC

## Author(s)

This application was written by Jon Ison (jison@hgmp.mrc.ac.uk)

## History

Written (Jan 2001) - Jon Ison.

## Target users

This program is intended to be run by EMBOSS site maintainers or those responsible for setting up and maintaining protein 3D structural data for use by others.

## Comments