'\" t .\" Title: JASPSCAN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "JASPSCAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "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" jaspscan \- Scans DNA sequences for transcription factors .SH "SYNOPSIS" .HP \w'\fBjaspscan\fR\ 'u \fBjaspscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-matrices\ \fR\fB\fIstring\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-exclude\ \fR\fB\fIstring\fR\fR] [\fB\-both\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBjaspscan\fR\ 'u \fBjaspscan\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBjaspscan\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Transcription" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-menu\fR \fIlist\fR .RS 4 Default value: C .RE .PP \fB\-matrices\fR \fIstring\fR .RS 4 The name \*(Aqall\*(Aq reads in all matrix files from the selected JASPAR matrix set\&. You can specify individual matrices by giving their names with commas between then, such as: \*(Aqma0001\&.1,ma0015*\*(Aq\&. The case of the names is not important\&. You can specify a file of matrix names to read in by giving the name of the file holding the matrix names with a \*(Aq@\*(Aq character in front of it, for example, \*(Aq@matrix\&.list\*(Aq\&. Blank lines and lines starting with a hash character or \*(Aq!\*(Aq are ignored and all other lines are concatenated together with a comma character \*(Aq,\*(Aq and then treated as the list of enzymes to search for\&. An example of a file of matrix names is: ! my matrices ma0001\&.1, ma0002\&.1 ! other matrices ma0010\&.1 ma0032* ma0053\&.1 Default value: all .RE .SS "Required section" .PP \fB\-threshold\fR \fIfloat\fR .RS 4 If the matrix score is greater than or equal to this percentage then a hit will be reported Default value: 80\&.0 .RE .SS "Additional section" .PP \fB\-exclude\fR \fIstring\fR .RS 4 The names of any matrices to exclude from the \*(Aqmatrices\*(Aq list\&. Matrices are specified in the same way as for the selection list\&. .RE .PP \fB\-both\fR \fIboolean\fR .RS 4 If set then both the forward and reverse strands are searched Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .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 jaspscan 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