'\" t .\" Title: SSEMATCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" 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" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .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