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domainnre - Online in the Cloud

Run domainnre in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command domainnre that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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