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:
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