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

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

AUTHOR

Debian Med Packaging Team <[email protected]>

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.