NAME

       domainseqs - Adds sequence records to a DCF file.

SYNOPSIS

       domainseqs -dcfinfile infile -dpdbdir directory -getswiss toggle -pdbtospfile infile
                  -datafile matrixf -gapopen float -gapextend float -dcfoutfile outfile
                  -logfile outfile

       domainseqs -help

DESCRIPTION

       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).

OPTIONS

   Input section
       -dcfinfile infile
           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.

       -dpdbdir directory
           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: ./

       -getswiss toggle
           Default value: N

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

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

   Required section
   Additional section
       -gapopen float
           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

       -gapextend float
           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

   Output section
       -dcfoutfile outfile
           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

       -logfile outfile
           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

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

       domainseqs 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.