GEF Primer Plugin ================= Goal ---- Create 1 primer pair around one annotation for many sequences Creator ------- Stephan Janosch janosch@mpi-cbg.de http://orcid.org/0000-0002-2401-6862 Options ------- name: 'taskOptions.designNewOptions.oligosToPickOptions.forwardOption' label: 'Forward Primer' default value: 'true' current value: 'true' possible values: 'true' or 'false' name: 'taskOptions.designNewOptions.oligosToPickOptions.probeOption' label: 'DNA Probe' default value: 'false' current value: 'false' possible values: 'true' or 'false' name: 'taskOptions.designNewOptions.oligosToPickOptions.reverseOption' label: 'Reverse Primer' default value: 'true' current value: 'true' possible values: 'true' or 'false' name: 'taskOptions.designWithExisting.designingForOption' label: '' default value: 'partnerForExisting' current value: 'partnerForExisting' possible values: partnerForExisting (Design a primer to match an existing one) () probeForPair (Design a probe for a pair of primers) () name: 'taskOptions.designWithExisting.existingPrimerOptions.existingPrimerOption' label: 'Existing:' default value: '' current value: '' name: 'taskOptions.designWithExisting.existingPairOptions.existingPairLeftOption' label: 'Forward:' default value: '' current value: '' name: 'taskOptions.designWithExisting.existingPairOptions.existingPairRightOption' label: 'Reverse:' default value: '' current value: '' name: 'taskOptions.chooser' label: 'Select Task:' default value: 'designNewOptions' current value: 'designNewOptions' possible values: designNewOptions (Design New) () designWithExisting (Design with Existing) () name: 'panelForRegionType.designRegionTypeOption' label: 'Task:' default value: 'genericOptionValue' current value: 'genericOptionValue' possible values: name: 'genericOptionValue' label: 'Generic' description: 'Standard primer design' name: 'cloningOptionValue' label: 'Precise' description: 'Designs primers to amplify a specific region, suitable for cloning' name: 'panelForRegionType.genericRegionOptions.customComponent1' label: '' default value: '' current value: '' name: 'panelForRegionType.genericRegionOptions.enableIncludedRegionOption' label: 'Included Region:' description: 'A sub-region of the given sequence in which primers are allowed to bind.' default value: 'false' current value: 'false' possible values: 'true' or 'false' name: 'panelForRegionType.genericRegionOptions.includedRegionFromOption' label: '' description: 'A sub-region of the given sequence in which primers are allowed to bind.' default value: '1' current value: '1' possible values: any integer between '1' and '92732' name: 'panelForRegionType.genericRegionOptions.label_1' label: '' default value: ' To ' current value: ' To ' name: 'panelForRegionType.genericRegionOptions.includedRegionToOption' label: '' description: 'A sub-region of the given sequence in which primers are allowed to bind.' default value: '1' current value: '46366' possible values: any integer between '1' and '92732' name: 'panelForRegionType.genericRegionOptions.allSelectionsAreBatchIncludedRegionsOption' label: 'Use all selections' description: 'Design a batch of primers using each selection as the included region.' default value: 'false' current value: 'false' possible values: 'true' or 'false' name: 'panelForRegionType.genericRegionOptions.customComponent2' label: '' default value: '' current value: '' name: 'panelForRegionType.genericRegionOptions.enableTargetRegionOption' label: 'Target Region:' description: 'The region of interest which primer pairs must amplify. Primers will not
bind inside this region unless "Allow primers inside" is turned on.' default value: 'false' current value: 'false' possible values: 'true' or 'false' name: 'panelForRegionType.genericRegionOptions.targetRegionFromOption' label: '' description: 'The region of interest which primer pairs must amplify. Primers will not
bind inside this region unless "Allow primers inside" is turned on.' default value: '1' current value: '1' possible values: any integer between '1' and '92732' name: 'panelForRegionType.genericRegionOptions.label_2' label: '' default value: ' To ' current value: ' To ' name: 'panelForRegionType.genericRegionOptions.targetRegionToOption' label: '' description: 'The region of interest which primer pairs must amplify. Primers will not
bind inside this region unless "Allow primers inside" is turned on.' default value: '1' current value: '1' possible values: any integer between '1' and '92732' name: 'panelForRegionType.genericRegionOptions.allSelectionsAreBatchTargetRegionsOption' label: 'Use all selections' description: 'Design a batch of primers using each selection as the target region.' default value: 'false' current value: 'false' possible values: 'true' or 'false' name: 'panelForRegionType.genericRegionOptions.customComponent3' label: '' default value: '' current value: '' name: 'panelForRegionType.genericRegionOptions.enableProductSizeOption' label: 'Product Size Between:' description: 'Limits the length of the PCR product.' default value: 'true' current value: 'true' possible values: 'true' or 'false' name: 'panelForRegionType.genericRegionOptions.productSizeFromOption' label: '' description: 'Limits the length of the PCR product.' default value: '1' current value: '1' possible values: any integer between '1' and '46366' name: 'panelForRegionType.genericRegionOptions.label_3' label: '' default value: ' And ' current value: ' And ' name: 'panelForRegionType.genericRegionOptions.productSizeToOption' label: '' description: 'Limits the length of the PCR product.' default value: '46366' current value: '46366' possible values: any integer between '1' and '46366' name: 'panelForRegionType.genericRegionOptions.customComponent4' label: '' default value: '' current value: '' name: 'panelForRegionType.genericRegionOptions.enableOptimalProductSizeOption' label: 'Optimal Product Size:' description: 'The preferred length of PCR product. For this to have effect,
the primer picking weight for optimal size must be > 0.' default value: 'false' current value: 'false' possible values: 'true' or 'false' name: 'panelForRegionType.genericRegionOptions.optimalProductSizeOption' label: '' description: 'The preferred length of PCR product. For this to have effect,
the primer picking weight for optimal size must be > 0.' default value: '1' current value: '1' possible values: any integer between '1' and '46366' name: 'panelForRegionType.genericRegionOptions.customComponent5' label: '' default value: '' current value: '' name: 'panelForRegionType.genericRegionOptions.label_4' label: '' default value: 'Number of pairs to generate:' current value: 'Number of pairs to generate:' name: 'panelForRegionType.genericRegionOptions.numPairsOption' label: '' default value: '5' current value: '5' possible values: any integer between '1' and '2147483647' name: 'saltConcentrationOptions.tmFormula' label: 'Formula:' description: 'Formula used to calculate the melting point of oligos' default value: '1' current value: '1' possible values: name: '0' label: 'Breslauer et al. 1986' description: 'Recommended for use with Phusion DNA polymerase' name: '1' label: 'SantaLucia 1998' description: 'Recommended by Primer3' name: 'saltConcentrationOptions.saltCorrectionFormula' label: 'Salt correction:' description: 'Salt correction formula used in calculating the melting point of oligos.' default value: '1' current value: '1' possible values: name: '0' label: 'Schildkraut and Lifson 1965' description: 'Used by older versions of Primer3' name: '1' label: 'SantaLucia 1998' description: 'Recommended by Primer3' name: '2' label: 'Owczarzy et al. 2004' name: 'saltConcentrationOptions.label_1' label: '' default value: '' current value: '' name: 'saltConcentrationOptions.divider_1' label: 'Concentration Settings' default value: '' current value: '' name: 'saltConcentrationOptions.monovalentSaltConcentration' label: 'Monovalent:' description: 'The millimolar concentration of monovalent salt cations' default value: '50.0' current value: '50.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'saltConcentrationOptions.annealingConc' label: 'Oligo:' description: 'The nanomolar concentration of each annealing oligo over the course of the PCR' default value: '50.0' current value: '50.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'saltConcentrationOptions.divalentSaltConcentration' label: 'Divalent:' description: 'The millimolar concentration of divalent salt cations' default value: '1.5' current value: '1.5' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'saltConcentrationOptions.dntpConcentration' label: 'dNTPs:' description: 'The millimolar concentration of deoxyribonucleotide triphosphate' default value: '0.6' current value: '0.6' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_WT_TM_LT' label: '' description: 'Penalty weight to use if melting point is less than optimal' default value: '1.0' current value: '1.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_WT_TM_GT' label: '' description: 'Penalty weight to use if melting point is greater than optimal' default value: '1.0' current value: '1.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_WT_SIZE_LT' label: '' description: 'Penalty weight to use if Size of primer is less than optimal' default value: '1.0' current value: '1.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_WT_SIZE_GT' label: '' description: 'Penalty weight to use if size of primer is greater than optimal' default value: '1.0' current value: '1.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_WT_GC_PERCENT_LT' label: '' description: 'Penalty weight to use if GC content point is less than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '100.0' name: 'characteristics.primerPenaltyWeights.PRIMER_WT_GC_PERCENT_GT' label: '' description: 'Penalty weight to use if GC content is greater than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '100.0' name: 'characteristics.primerPenaltyWeights.PRIMER_PAIR_WT_PRODUCT_TM_LT' label: '' description: 'Penalty weight to use if melting point of product less than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_PAIR_WT_PRODUCT_TM_GT' label: '' description: 'Penalty weight to use if melting point of product greater than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_PAIR_WT_PRODUCT_SIZE_LT' label: '' description: 'Penalty weight to use if size of product less than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_PAIR_WT_PRODUCT_SIZE_GT' label: '' description: 'Penalty weight to use if size of product greater than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_WT_END_STABILITY' label: '3' Stability:' description: 'Penalty for non optimal 3' stability' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_PAIR_WT_DIFF_TM' label: 'Melting Point Diff:' description: 'Penalty for non optimal melting point difference between forward and reverse' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_PAIR_WT_PR_PENALTY' label: 'Primer Penalty:' description: 'Weight of the Primer penalty in determining overall pair penalty' default value: '1.0' current value: '1.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_PAIR_WT_IO_PENALTY' label: 'DNA Probe penalty:' description: 'Weight of the DNA Probe penalty in determining overall pair penalty. Disabled when not designing a probe.' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PRIMER_DIMER_WT' label: 'Dimer Tm:' description: 'Penalty weight to use if hairpin/dimer Tm is greater than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.primerPenaltyWeights.PAIR_DIMER_WT' label: 'Dimer Tm:' description: 'Penalty weight to use if hairpin/dimer Tm is greater than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.probePenaltyWeights.PRIMER_IO_WT_TM_LT' label: '' description: 'Penalty weight to use if melting point is less than optimal' default value: '1.0' current value: '1.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.probePenaltyWeights.PRIMER_IO_WT_TM_GT' label: '' description: 'Penalty weight to use if melting point is greater than optimal' default value: '1.0' current value: '1.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.probePenaltyWeights.PRIMER_IO_WT_SIZE_LT' label: '' description: 'Penalty weight to use if size of probe is less than optimal' default value: '1.0' current value: '1.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.probePenaltyWeights.PRIMER_IO_WT_SIZE_GT' label: '' description: 'Penalty weight to use if size of probe is greater than optimal' default value: '1.0' current value: '1.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.probePenaltyWeights.PRIMER_IO_WT_GC_PERCENT_LT' label: '' description: 'Penalty weight to use if GC content is less than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '100.0' name: 'characteristics.probePenaltyWeights.PRIMER_IO_WT_GC_PERCENT_GT' label: '' description: 'Penalty weight to use if GC content is greater than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '100.0' name: 'characteristics.probePenaltyWeights.PROBE_DIMER_WT' label: 'Dimer Tm' description: 'Penalty weight to use if hairpin/dimer Tm is greater than optimal' default value: '0.0' current value: '0.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.ALLOW_INSIDE' label: 'Allow primers inside target with penalty:' description: 'Allow primers to overlap the target region' default value: 'false' current value: 'false' possible values: 'true' or 'false' name: 'characteristics.PRIMER_INSIDE_PENALTY' label: '' default value: '1.0' current value: '1.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_MIN_SIZE' label: 'Minimum primer size' default value: '18' current value: '18' possible values: any integer between '1' and '36' name: 'characteristics.advancedPrimerInputOptions.PRIMER_OPT_SIZE' label: 'Preferred primer size' default value: '20' current value: '20' possible values: any integer between '1' and '36' name: 'characteristics.advancedPrimerInputOptions.PRIMER_MAX_SIZE' label: 'Maximum primer size' default value: '27' current value: '27' possible values: any integer between '1' and '36' name: 'characteristics.advancedPrimerInputOptions.PRIMER_MIN_TM' label: 'Minimum primer Tm' default value: '57.0' current value: '57.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_OPT_TM' label: 'Preferred primer Tm' default value: '60.0' current value: '60.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_MAX_TM' label: 'Maximum primer Tm' default value: '63.0' current value: '63.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_MIN_GC' label: 'Minimum GC% base content in primer' default value: '20.0' current value: '20.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_OPT_GC_PERCENT' label: 'Preferred GC% base content in primer' default value: '50.0' current value: '50.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_MAX_GC' label: 'Maximum GC% base content in primer' default value: '80.0' current value: '80.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.primerDimerTm' label: 'Max Primer Dimer Tm' default value: '47.0' current value: '47.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_MAX_POLY_X' label: '' default value: '5' current value: '5' possible values: any integer between '1' and '36' name: 'characteristics.advancedPrimerInputOptions.PRIMER_PRODUCT_MIN_TM' label: 'Minimum product Tm' default value: '0.0' current value: '0.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_PRODUCT_OPT_TM' label: 'Preferred product Tm' default value: '0.0' current value: '0.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_PRODUCT_MAX_TM' label: 'Maximum product Tm' default value: '0.0' current value: '0.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_GC_CLAMP' label: '' default value: '0' current value: '0' possible values: any integer between '0' and '36' name: 'characteristics.advancedPrimerInputOptions.PRIMER_MAX_DIFF_TM' label: '' default value: '100.0' current value: '100.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.advancedPrimerInputOptions.PRIMER_MAX_END_STABILITY' label: '' description: 'Maximum delta G (kcal/mol) for duplex disruption for the
five 3' bases as calculated using the specified Tm formula.' default value: '9.0' current value: '9.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.advancedProbeInputOptions.PRIMER_INTERNAL_OLIGO_MIN_SIZE' label: 'Minimum probe size' default value: '18' current value: '18' possible values: any integer between '1' and '36' name: 'characteristics.advancedProbeInputOptions.PRIMER_INTERNAL_OLIGO_OPT_SIZE' label: 'Preferred probe size' default value: '20' current value: '20' possible values: any integer between '1' and '36' name: 'characteristics.advancedProbeInputOptions.PRIMER_INTERNAL_OLIGO_MAX_SIZE' label: 'Maximum probe size' default value: '27' current value: '27' possible values: any integer between '1' and '36' name: 'characteristics.advancedProbeInputOptions.PRIMER_INTERNAL_OLIGO_MIN_TM' label: 'Minimum probe Tm' default value: '57.0' current value: '57.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedProbeInputOptions.PRIMER_INTERNAL_OLIGO_OPT_TM' label: 'Preferred probe Tm' default value: '60.0' current value: '60.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedProbeInputOptions.PRIMER_INTERNAL_OLIGO_MAX_TM' label: 'Maximum probe Tm' default value: '63.0' current value: '63.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedProbeInputOptions.PRIMER_INTERNAL_OLIGO_MIN_GC' label: 'Minimum GC% base content in probe' default value: '20.0' current value: '20.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedProbeInputOptions.PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT' label: 'Preferred GC% base content in probe' default value: '50.0' current value: '50.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedProbeInputOptions.PRIMER_INTERNAL_OLIGO_MAX_GC' label: 'Maximum GC% base content in probe' default value: '80.0' current value: '80.0' possible values: any double between '-1.7976931348623157E308' and '1.7976931348623157E308' name: 'characteristics.advancedProbeInputOptions.primerDimerTm' label: 'Max Primer Dimer Tm' default value: '47.0' current value: '47.0' possible values: any double between '0.0' and '1.7976931348623157E308' name: 'characteristics.advancedProbeInputOptions.PRIMER_INTERNAL_OLIGO_MAX_POLY_X' label: '' default value: '5' current value: '5' possible values: any integer between '1' and '36' name: 'characteristics.degeneracy.allowDegeneracyOption' label: 'Allow Degeneracy: ' default value: 'false' current value: 'false' possible values: 'true' or 'false' name: 'characteristics.degeneracy.maxDegeneracyOption' label: '' default value: '1' current value: '1' possible values: any integer between '1' and '2147483647' name: 'extension.forwardExtensionButton' label: '' default value: 'Fwd: none' current value: 'Fwd: none' name: 'extension.forwardExtension.addBases' label: '' default value: 'Bases...' current value: 'Bases...' name: 'extension.forwardExtension.addRestriction Site' label: '' default value: 'Restriction Site...' current value: 'Restriction Site...' name: 'extension.forwardExtension.addGateway Site' label: '' default value: 'Gateway Site...' current value: 'Gateway Site...' name: 'extension.forwardExtension.extensions' label: '' default value: '' current value: '' name: 'extension.reverseExtensionButton' label: '' default value: 'Rev: none' current value: 'Rev: none' name: 'extension.reverseExtension.addBases' label: '' default value: 'Bases...' current value: 'Bases...' name: 'extension.reverseExtension.addRestriction Site' label: '' default value: 'Restriction Site...' current value: 'Restriction Site...' name: 'extension.reverseExtension.addGateway Site' label: '' default value: 'Gateway Site...' current value: 'Gateway Site...' name: 'extension.reverseExtension.extensions' label: '' default value: '' current value: '' name: 'extension.misprimingLibrary' label: '' description: 'Select a library of repeats which primers should not amplify.' default value: 'none' current value: 'none' possible values: name: 'none' label: 'None' name: 'human_and_simple' label: 'Human' description: 'Contains microsatellites' name: 'rodent_and_simple' label: 'Rodent and Simple' description: 'Contains microsatellites' name: 'rodent' label: 'Rodent' description: 'No microsatellites' name: 'drosophila' label: 'Drosophila' name: 'custom' label: 'Custom library' description: '(fasta format)' name: 'extension.customLibrary' label: '' description: 'The location of the fasta file containing the mispriming library' default value: '/Users/janosch/dev/geneiousPlugins/geneious-10.2.3-devkit/examples/GeneiousFiles/bundledPlugins/com.biomatters.plugins.primerDesign.PrimerDesignPlugin/com/biomatters/plugins/primerDesign/mispriming_libraries/human_and_simple.fasta' current value: '/Users/janosch/dev/geneiousPlugins/geneious-10.2.3-devkit/examples/GeneiousFiles/bundledPlugins/com.biomatters.plugins.primerDesign.PrimerDesignPlugin/com/biomatters/plugins/primerDesign/mispriming_libraries/human_and_simple.fasta' possible values: any valid filename name: 'extension.maxMispriming' label: '' description: 'The maximum allowed weighted similarity with any sequence in Mispriming Library' default value: '12.0' current value: '12.0' possible values: any double between '0.0' and '100.0' name: 'extension.maxMisprimingPair' label: 'Pair:' description: 'The maximum allowed sum of similarities of a primer pair (one similarity for each primer) with any single sequence in the mispriming library.
Library sequence weights are not used in computing the sum of similarities.' default value: '24.0' current value: '24.0' possible values: any double between '0.0' and '100.0' name: 'applyToReferencedSequences' label: 'When run on alignments/contigs, apply annotations to referenced sequences' default value: 'false' current value: 'false' possible values: 'true' or 'false'