prima1e
Selects primers for pcr and dna amplification.
Usage
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
Overview
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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.
-maxpgccont since Debian 6.0 (Squeeze);
-maxplen since Debian 6.0 (Squeeze);
-maxtmprimer since Debian 6.0 (Squeeze);
-minpgccont since Debian 6.0 (Squeeze);
-minplen since Debian 6.0 (Squeeze);
-mintmprimer since Debian 6.0 (Squeeze).
-maxprimertm until Debian 5.0 (Lenny);
-maxprodgccont until Debian 5.0 (Lenny);
-maxprodlen until Debian 5.0 (Lenny);
-minprimertm until Debian 5.0 (Lenny);
-minprodgccont until Debian 5.0 (Lenny);
-minprodlen until Debian 5.0 (Lenny).