Primer Z


Bioinformatics Pipeline for IBMS Genetic Research
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v3.1 Jun 2007

Primer Z:
streamlined primer design for promoters, exons and human SNPs

Tsai, M.F., Lin, Y.J., Cheng, Y.C., Lee, K.H., Huang, C.C., Chen, Y.T. and Yao, Adam (2007) PrimerZ: streamlined primer design for promoters, exons and human SNPs, Nucleic Acids Research, doi:10.1093/nar/gkm383 Full Text

Primer for

Species

Human Mouse

Gene Name or Ensembl ID

Chr.
Range:from to

example
ex. ACE or ENSG00000159640

SNP Flank Sequence Length

Promoter Region

Upstream of gene: valid format is 0~1000000

Maximum Exon Length

Maximum Length

Exon Flanking sequences Length

Flanking sequences Length

Product Size Ranges

Excluded Regions

Advance Options

General Primer Picking Conditions

Mispriming Library (repeat library):

Primer Size	Min: Opt: Max:
Primer Tm	Min: Opt: Max:	Max Tm Difference:
Product Tm	Min: Opt: Max:
Primer GC%	Min: Opt: Max:

Max Self Complementarity:		Max 3' Self Complementarity:
Max #N's:		Max Poly-X:
Inside Target Penalty:		Outside Target Penalty:
First Base Index:		CG Clamp:
Salt Concentration:		Annealing Oligo Concentration:
Number To Return:		Max 3' Stability:
Max Repeat Mispriming:		Pair Max Repeat Mispriming
Max Template Mispriming		Pair Max Template Mispriming

Other Per-Sequence Inputs

Included Region:		E.g. 20,400: only pick primers in the 400 base region starting at position 20.
Start Codon Position:

Sequence Quality

Min Sequence Quality:		Min End Sequence Quality:
Sequence Quality Range Min:		Sequence Quality Range Max:

Objective Function Penalty Weights for Primers

Tm:

Lt: Gt:

Size:

Lt: Gt:

GC%:

Lt: Gt:

Self Complementarity:

3' Self Complementarity:		#N's:
Mispriming:		Sequence Quality:
End Sequence Quality:		Position Penalty:
End Stability:		Template Mispriming:

Objective Function Penalty Weights for Primer Pairs

Product Size:

Lt: Gt:

Product Tm:

Lt: Gt:

Tm Difference:		Any Complementarity:
3' Complementarity:		Pair Mispriming:
Primer Penalty Weight:		Hyb Oligo Penalty Weight:
Primer Pair Template Mispriming Weight:

Hyb Oligo (Internal Oligo)

Hyb Oligo (Internal Oligo) Per-Sequence Inputs

Hyb Oligo Excluded Region:

Hyb Oligo (Internal Oligo) General Conditions

Hyb Oligo Size:	Min: Opt: Max:
Hyb Oligo Tm:	Min: Opt: Max:
Hyb Oligo GC%:	Min: Opt: Max:
Hyb Oligo Mishyb Library:

Hyb Oligo Self Complementarity:		Hyb Oligo Max 3' Self Complementarity:
Max #Ns:		Hyb Oligo Max Poly-X:
Hyb Oligo Max Mishyb:		Hyb Oligo Salt Concentration:
Hyb Oligo DNA Concentration:

Objective Function Penalty Weights for Hyb Oligos (Internal Oligos)

Hyb Oligo Tm:	Lt: Gt:	Hyb Oligo Size:	Lt: Gt:
Hyb Oligo GC%:	Lt: Gt:

Hyb Oligo Self Complementarity:		Hyb Oligo #N's:
Hyb Oligo Mishybing:		Hyb Oligo Sequence Quality: