Primer Z

"FANS: Functional Analysis of Novel SNPs and Mutations in Human and Mouse Genomes" has been provisionally accepted, and will be published in BMC Bioinformatics. Welcome to visit and try the FANS website at http://fans.ngc.sinica.edu.tw/
	Bioinformatics Pipeline for IBMS Genetic Research
	NCBI 36.3 / UCSC hg18 / Ensembl v50	Home	Info	About Us	Help

Run GenePipe

QualiSeq

GenoWatch

VisualSNP

PrimerZ

Affyrmation

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: