NAME

       domainnr - Removes redundant domains from a DCF file.

SYNOPSIS

       domainnr -dcfinfile infile [-datafile matrixf] -retain toggle -node list -mode list
                -threshold float -threshlow float -threshup float [-gapopen float]
                [-gapextend float] -dcfoutfile outfile -redoutfile outfile -logfile outfile

       domainnr -help

DESCRIPTION

       domainnr 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 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.

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

       -retain toggle
           This option specifies whether to write redundant domains to a separate file. If this
           option is selected, redundant domains are written to a separate output file. Default
           value: N

   Required section
       -node list
           This option specifies the node for redundancy removal. Redundancy can be removed at
           any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class'
           entries belonging to the same Class will be non-redundant. Default value: 1

       -mode list
           This option specifies whether to remove redundancy at a single threshold % sequence
           similarity or remove redundancy outside a range of acceptable threshold % similarity.
           All permutations of pair-wise sequence alignments are calculated for each domain
           family in turn using the EMBOSS implementation of the Needleman and Wunsch global
           alignment algorithm. Redundant sequences are removed in one of two modes as follows:
           (i) If a pair of proteins achieve greater than a threshold percentage sequence
           similarity (specified by the user) the shortest sequence is discarded. (ii) If a pair
           of proteins have a percentage sequence similarity that lies outside an acceptable
           range (specified by the user) the shortest sequence is discarded. Default value: 1

       -threshold float
           This option specifies the % sequence identity redundancy threshold, which determines
           the redundancy calculation. If a pair of proteins achieve greater than this threshold
           the shortest sequence is discarded. Default value: 95.0

       -threshlow float
           This option specifies the % sequence identity redundancy threshold, which determines
           the redundancy calculation. If a pair of proteins have a percentage sequence
           similarity that lies outside an acceptable range the shortest sequence is discarded.
           Default value: 30.0

       -threshup float
           This option specifies the % sequence identity redundancy threshold, which determines
           the redundancy calculation. If a pair of proteins have a percentage sequence
           similarity that lies outside an acceptable range the shortest sequence is discarded.
           Default value: 90.0

   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

   Advanced section
   Output section
       -dcfoutfile outfile
           This option specifies the name of non-redundant 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: test.scop

       -redoutfile outfile
           This option specifies the name of DCF file (domain classification file) for redundant
           sequences (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 log file for the build. The log file contains
           messages about any errors arising while domainnr ran. Default value: domainnr.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

       domainnr 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.