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.