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

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_

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 percentage sequence identity redundancy threshold.

[-datafile] (matrixf)

This is the scoring matrix file used when comparing sequences.

[-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. You can usually expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception occurs when one or both sequences are single reads with possible sequencing errors, in which case you should expect many single base gaps. You can obtain this result by setting the gap open penalty to zero (or a very low value) and using the gap extension penalty to control gap scoring.

[-scopout] (outfile)

Name of nonredundant scop file for output (EMBL-like format).

[-errf] (outfile)

Name of log file for the build.