'\" t .\" Title: SIXPACK .\" 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 "SIXPACK" "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" sixpack \- Display a DNA sequence with 6\-frame translation and ORFs .SH "SYNOPSIS" .HP \w'\fBsixpack\fR\ 'u \fBsixpack\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-firstorf\ \fR\fB\fIboolean\fR\fR] [\fB\-lastorf\ \fR\fB\fIboolean\fR\fR] [\fB\-mstart\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-orfminsize\ \fR\fB\fIinteger\fR\fR \fB\-uppercase\ \fR\fB\fIrange\fR\fR \fB\-highlight\ \fR\fB\fIrange\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR .HP \w'\fBsixpack\fR\ 'u \fBsixpack\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsixpack\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Translation,Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Additional section" .PP \fB\-table\fR \fIlist\fR .RS 4 Genetics code used for the translation .RE .PP \fB\-firstorf\fR \fIboolean\fR .RS 4 Count the beginning of a sequence as a possible ORF, even if it\*(Aqs inferior to the minimal ORF size\&. Default value: Y .RE .PP \fB\-lastorf\fR \fIboolean\fR .RS 4 Count the end of a sequence as a possible ORF, even if it\*(Aqs not finishing with a STOP, or inferior to the minimal ORF size\&. Default value: Y .RE .PP \fB\-mstart\fR \fIboolean\fR .RS 4 Displays only ORFs starting with an M\&. Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 ORF sequence output .RE .PP \fB\-reverse\fR \fIboolean\fR .RS 4 Display also the translation of the DNA sequence in the 3 reverse frames Default value: Y .RE .PP \fB\-orfminsize\fR \fIinteger\fR .RS 4 Minimum size of Open Reading Frames (ORFs) to display in the translations\&. Default value: 1 .RE .PP \fB\-uppercase\fR \fIrange\fR .RS 4 Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 .RE .PP \fB\-highlight\fR \fIrange\fR .RS 4 Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .PP \fB\-number\fR \fIboolean\fR .RS 4 Number the sequence at the beginning and the end of each line\&. Default value: Y .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 Number of nucleotides displayed on each line Default value: 60 .RE .PP \fB\-length\fR \fIinteger\fR .RS 4 .RE .PP \fB\-margin\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the ID name of the sequence\&. Default value: Y .RE .PP \fB\-description\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the description of the sequence\&. Default value: Y .RE .PP \fB\-offset\fR \fIinteger\fR .RS 4 Number from which you want the DNA sequence to be numbered\&. Default value: 1 .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .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 sixpack 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