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 infile
This 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 integer
This option specifies the number of top-scoring matches to report. Default value: 5
Additional section
-rgapopen float
This 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 outfile
This 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.
DOMAINATRIX 0.1.0+20100721 08/11/2010 SSEMATCH(1e)