NAME¶
primers - Simple version of primer3 to pick PCR primers
SYNOPSIS¶
primers -sequence seqall
[-targetregion range]
[-minsize integer]
[-maxsize integer]
[-maxdifftm float]
[-explainflag boolean]
[-numreturn integer]
-outfile outfile
primers -help
DESCRIPTION¶
primers is a command line program from EMBOSS (“the
European Molecular Biology Open Software Suite”). It is part of the
"Nucleic:Primers" command group(s).
OPTIONS¶
-sequence seqall
The sequence from which to choose primers. The sequence
must be presented 5' -> 3'
Additional section¶
-targetregion range
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.
-minsize integer
Minimum acceptable length of a primer. Must be greater
than 0 and less than or equal to MAX-SIZE. Default value: 18
-maxsize integer
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's melting-temperature is valid.
Default value: 27
-maxdifftm float
Maximum acceptable (unsigned) difference between the
melting temperatures of the forward and reverse primers. Default value:
100.0
Output section¶
-explainflag boolean
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
-numreturn integer
The maximum number of primer pairs to return. Primer
pairs returned are sorted by their 'quality', 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
-outfile outfile
SEE ALSO¶
primers is fully documented via the tfm(1) system.
AUTHOR¶
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
COPYRIGHT¶
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.
