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'\" t
.\" Title: SSEMATCH
.\" Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
.\" Date: 08/11/2010
.\" Manual: EMBOSS Manual for Debian
.\" Source: DOMAINATRIX 0.1.0+20100721
.\" Language: English
.\"
.TH "SSEMATCH" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian"
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.el .ds Aq '
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.nh
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.\" * MAIN CONTENT STARTS HERE *
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.SH "NAME"
ssematch \- Search a DCF file for secondary structure matches\&.
.SH "SYNOPSIS"
.HP \w'\fBssematch\fR\ 'u
\fBssematch\fR \fB\-ssinfile\ \fR\fB\fIinfile\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-maxhits\ \fR\fB\fIinteger\fR\fR [\fB\-rgapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-rgapextend\ \fR\fB\fIfloat\fR\fR] [\fB\-egapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-egapextend\ \fR\fB\fIfloat\fR\fR] \fB\-outssfile\ \fR\fB\fIoutfile\fR\fR \fB\-outsefile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBssematch\fR\ 'u
\fBssematch\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBssematch\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-ssinfile\fR \fIinfile\fR
.RS 4
This option specifies the name of the file of secondary structure (input)\&.
.RE
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
This option specifies the name of the DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq 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\&.
.RE
.PP
\fB\-datafile\fR \fImatrixf\fR
.RS 4
This option specifies the secondary structure substitution matrix\&. Default value: SSSUB
.RE
.SS "Required section"
.PP
\fB\-maxhits\fR \fIinteger\fR
.RS 4
This option specifies the number of top\-scoring matches to report\&. Default value: 5
.RE
.SS "Additional section"
.PP
\fB\-rgapopen\fR \fIfloat\fR
.RS 4
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
.RE
.PP
\fB\-rgapextend\fR \fIfloat\fR
.RS 4
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
.RE
.PP
\fB\-egapopen\fR \fIfloat\fR
.RS 4
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
.RE
.PP
\fB\-egapextend\fR \fIfloat\fR
.RS 4
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
.RE
.SS "Output section"
.PP
\fB\-outssfile\fR \fIoutfile\fR
.RS 4
This option specifies the name of the file containing top\-scoring domains for residue\-based alignment (output)\&.A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&.
.RE
.PP
\fB\-outsefile\fR \fIoutfile\fR
.RS 4
This option specifies the name of the file containing top\-scoring domains for secondary structure element\-based alignment (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&.
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
.RS 4
This option specifies the name of the ssematch log file (output)\&. Default value: ssematch\&.log
.RE
.SH "BUGS"
.PP
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)\&.
.SH "SEE ALSO"
.PP
ssematch is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
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\&.
.sp
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