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'\" t
.\" Title: PRIMERS
.\" Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\" Date: 05/11/2012
.\" Manual: EMBOSS Manual for Debian
.\" Source: EMBOSS 6.4.0
.\" Language: English
.\"
.TH "PRIMERS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
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.\" http://bugs.debian.org/507673
.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
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.ie \n(.g .ds Aq \(aq
.el .ds Aq '
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.nh
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.\" * MAIN CONTENT STARTS HERE *
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.SH "NAME"
primers \- Simple version of primer3 to pick PCR primers
.SH "SYNOPSIS"
.HP \w'\fBprimers\fR\ 'u
\fBprimers\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-targetregion\ \fR\fB\fIrange\fR\fR] [\fB\-minsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxdifftm\ \fR\fB\fIfloat\fR\fR] [\fB\-explainflag\ \fR\fB\fIboolean\fR\fR] [\fB\-numreturn\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBprimers\fR\ 'u
\fBprimers\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBprimers\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-sequence\fR \fIseqall\fR
.RS 4
The sequence from which to choose primers\&. The sequence must be presented 5\*(Aq \-> 3\*(Aq
.RE
.SS "Additional section"
.PP
\fB\-targetregion\fR \fIrange\fR
.RS 4
If one or more Targets is specified then a legal primer pair must flank at least one of them\&. A Target might be a simple sequence repeat site (for example a CA repeat) or a single\-base\-pair polymorphism\&. The value should be a space\-separated list of <start>,<end> pairs where <start> is the index of the first base of a Target, and <end> is the last E\&.g\&. 50,51 requires primers to surround the 2 bases at positions 50 and 51\&.
.RE
.PP
\fB\-minsize\fR \fIinteger\fR
.RS 4
Minimum acceptable length of a primer\&. Must be greater than 0 and less than or equal to MAX\-SIZE\&. Default value: 18
.RE
.PP
\fB\-maxsize\fR \fIinteger\fR
.RS 4
Maximum acceptable length (in bases) of a primer\&. Currently this parameter cannot be larger than 35\&. This limit is governed by the maximum oligo size for which Primer3\*(Aqs melting\-temperature is valid\&. Default value: 27
.RE
.PP
\fB\-maxdifftm\fR \fIfloat\fR
.RS 4
Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers\&. Default value: 100\&.0
.RE
.SS "Output section"
.PP
\fB\-explainflag\fR \fIboolean\fR
.RS 4
If this flag is non\-0, produce LEFT\-EXPLAIN and RIGHT\-EXPLAIN, output, which are intended to provide information on the number of primer pairs that Primer3 examined, and statistics on the number discarded for various reasons\&. Default value: N
.RE
.PP
\fB\-numreturn\fR \fIinteger\fR
.RS 4
The maximum number of primer pairs to return\&. Primer pairs returned are sorted by their \*(Aqquality\*(Aq, in other words by the value of the objective function (where a lower number indicates a better primer pair)\&. Caution: setting this parameter to a large value will increase running time\&. Default value: 5
.RE
.PP
\fB\-outfile\fR \fIoutfile\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
primers 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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