SSEMATCH(1e) | EMBOSS Manual for Debian | SSEMATCH(1e) |
NAME¶
ssematch - Search a DCF file for secondary structure matches.SYNOPSIS¶
ssematch
-ssinfile infile
-dcfinfile infile [
-datafile matrixf]
-maxhits integer [
-rgapopen float] [
-rgapextend float]
[-egapopen float] [
-egapextend float]
-outssfile outfile
-outsefile outfile
-logfile outfile
ssematch
-help
DESCRIPTION¶
ssematch 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¶
-ssinfile infileThis option specifies the name of the file of
secondary structure (input).
-dcfinfile infile
This option specifies the name of the 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 secondary structure
substitution matrix. Default value: SSSUB
Required section¶
-maxhits integerThis option specifies the number of
top-scoring matches to report. Default value: 5
Additional section¶
-rgapopen floatThis options specifies the gap insertion
penalty for reside-based alignment. The gap insertion penalty 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
-rgapextend float
This options specifies the gap extension
penalty for residue-based alignment. The gap extension, penalty 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
-egapopen float
This options specifies the gap insertion
penalty for element-based alignment. The gap insertion penalty 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
-egapextend float
This options specifies the gap extension
penalty for secondary structure element-based alignment. The gap extension,
penalty 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¶
-outssfile outfileThis option specifies the name of the file
containing top-scoring domains for residue-based alignment (output).A 'domain
classification file' contains classification and other data for domains from
SCOP or CATH, in DCF format (EMBL-like).
-outsefile outfile
This option specifies the name of the file
containing top-scoring domains for secondary structure element-based alignment
(output). A 'domain classification file' contains classification and other
data for domains from SCOP or CATH, in DCF format (EMBL-like).
-logfile outfile
This option specifies the name of the ssematch
log file (output). Default value: ssematch.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¶
ssematch 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.08/11/2010 | DOMAINATRIX 0.1.0+20100721 |