This is the command primerse that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Input section
-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
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