domainseqs - Adds sequence records to a DCF file.

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DOMAINATRIX 0.1.0+20100721                         08/11/2010                                     DOMAINSEQS(1e)

domainseqs is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”).
       It is part of the "Utils:Database creation" command group(s).

       domainseqs - Adds sequence records to a DCF file.

Inputsection-dcfinfileinfile
           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.

       -dpdbdirdirectory
           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. Default value:
           ./

       -getswisstoggle
           Default value: N

       -pdbtospfileinfile
           This option specifies the name of the pdbcodes to swissprot indexing file. The swissprot:PDB
           equivalence file is generated by PDBTOSP

       -datafilematrixf
           This option specifies the residue substitution matrix, which is used for sequence comparison. Default
           value: EBLOSUM62

   RequiredsectionAdditionalsection-gapopenfloat
           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. Default
           value: 10

       -gapextendfloat
           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.
           Default value: 0.5

   Outputsection-dcfoutfileoutfile
           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. Default value: domainseqs.out

       -logfileoutfile
           This option specifies the name of log file for the build. The log file contains messages about any
           errors arising while domainseqs ran. Default value: domainseqs.log

       domainseqs is fully documented via the tfm(1) system.

domainseqs-dcfinfileinfile-dpdbdirdirectory-getswisstoggle-pdbtospfileinfile-datafilematrixf-gapopenfloat-gapextendfloat-dcfoutfileoutfile-logfileoutfiledomainseqs-help