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PRIMA(1e) EMBOSS Manual for Debian PRIMA(1e)

NAME

prima - Selects primers for PCR and DNA amplification.

SYNOPSIS

prima -sequence sequence -targetrange toggle -targetstart integer -targetend integer -mintmprimer float -maxtmprimer float -minplen  integer -maxplen integer -minpgccont  float -maxpgccont  float [-primer  toggle] -minprimerlen integer -maxprimerlen integer -minpmgccont float -maxpmgccont float -overlap  integer -saltconc  float -dnaconc float -list boolean -outfile outfile

prima -help

DESCRIPTION

prima 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 sequence

Required section

Target options

-targetrange toggle
Default value: N

-targetstart integer

Default value: $(sequence.begin)

-targetend integer

Default value: $(sequence.length)

-mintmprimer float

Default value: 53

-maxtmprimer float

Default value: 58

Additional section

Product options

-minplen integer
Default value: 100

-maxplen integer

Default value: 300

-minpgccont float

Default value: .40

-maxpgccont float

Default value: .55

Primer options

-primer toggle
Specify primer properties Default value: Y

-minprimerlen integer

Default value: 18

-maxprimerlen integer

Default value: 22

-minpmgccont float

Default value: .40

-maxpmgccont float

Default value: .55

Advanced section

-overlap integer
Default value: 50

-saltconc float

Default value: 50

-dnaconc float

Default value: 50

-list boolean

Default value: N

Output section

-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

prima 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.

05/11/2012 EMBOSS 6.4.0