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

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.

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