bionic (1) primers.1e.gz

Provided by: emboss_6.6.0+dfsg-6build1_amd64 bug

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


BUGS
       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).


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.


       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.