PrimerZ | Tool name | PrimerZ |
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| URL | http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do |
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| Important features | 1. Designs primers for exon, promoters, and human SNPs.
2. Provides chromosomal location of the gene, allows for SNP checking and avoids the regions with SNP's for primer designing. Provides promoter location also.
3. Displays the location of target gene in the chromosome and the transcript variants of the target gene [graphical representation]. |
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| Citations | Tsai MF, Lin YJ, Cheng YC, Lee KH, Huang CC, Chen YT, Yao A. PrimerZ:
streamlined primer design for promoters, exons and human SNPs. Nucleic Acids Res.
2007 Jul;35(Web Server issue):W63-5. Epub 2007 May 30. PubMed PMID: 17537812;
PubMed Central PMCID: PMC1933185. |
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| Year of publication | 2007 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | Junction primers, SNP primers, Primer specificity checking, Masking the repeat sequence, Predicting secondary structure |
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| Category | Online, Free |
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| Features | 1. Options to set the primer parameters such as Tm, Tm difference, GC%, mis-priming library, max self complementary, max 3 prime end stability, max repeat sequence allowed, salt concentration, etc.
2. Options to specify the promoter region, exon length, exon flanking sequence, product size range etc.
3. Designs primers to a specific region mentioned by the users.
4. Allows the user to specify the penalty weights for primer parameters.
5. Also designs internal oligo.
6. It has the link to dbSNP database to check the SNP details.
7. It has the link to USCS in silico browser to check the Tm of the primer and the salt concentration at which the primer Tm was calculated.
8. Also provides the promoter information. |
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| Description | |
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