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domainsse(1e) [debian man page]

DOMAINSSE(1e)						     EMBOSS Manual for Debian						     DOMAINSSE(1e)

NAME

       domainsse - Add secondary structure records to a DCF file.

SYNOPSIS

       domainsse -dcfinfile infile -dccfdir directory -dcfoutfile outfile -logfile outfile

       domainsse -help

DESCRIPTION

       domainsse 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).

OPTIONS

   Input section
       -dcfinfile infile
	   This option specifies the name of the 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.

       -dccfdir directory
	   This option specifies the location of the domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein
	   coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean
	   coordinate file'), 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: ./

   Required section
   Advanced section
   Output section
       -dcfoutfile outfile
	   This option specifies the name of the DCF file (domain classification file) with secondary structure records (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.

       -logfile outfile
	   This option specifies the name of the DOMAINSSE log file. Default value: domainsse.log

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

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

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
	   Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as
       EMBOSS itself.

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

Check Out this Related Man Page

SEQWORDS(1e)						     EMBOSS Manual for Debian						      SEQWORDS(1e)

NAME

       seqwords - Generates DHF files from keyword search of UniProt.

SYNOPSIS

       seqwords -keyfile infile -spfile infile -outfile outfile

       seqwords -help

DESCRIPTION

       seqwords is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Protein:3D
       Structure" command group(s).

OPTIONS

   Input section
       -keyfile infile
	   This option specifies the name of keywords file (input). This contains a list of keywords specific to a number of SCOP or CATH families
	   and superfamilies used by SEQWORDS to search a sequence database.

       -spfile infile
	   This option specifies the name of the sequence database (input) to search.

   Output section
       -outfile outfile
	   This option specifies the name of the DHF file (domain hits file) (output). A 'domain hits file' contains database hits (sequences)
	   with domain classification information, in the DHF format (FASTA-like). The hits are relatives to a SCOP or CATH family (or other node
	   in the structural hierarchies) and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are
	   generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by
	   using LIBSCAN. Default value: test.hits

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

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

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
	   Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as
       EMBOSS itself.

DOMSEARCH 0.1.0++20100721					    08/11/2010							      SEQWORDS(1e)
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