Primer Premier

Primer Premier software combines design of primers for various PCR applications under one common platform. The software supports design of degenerate primers on alignments for amplifying a related set of nucleotide sequences for detecting many common traits amongst organisms and to determine heredity.[1]

Primer Premier
Developer(s)Premier Biosoft
Stable release
6.24
Operating systemWindows, Mac OS X
TypeBioinformatics
Licensecommercial
Websitehttp://www.premierbiosoft.com

The software also designs tagged and nested primers for multiplex PCR reactions.[2]

The Primer Premier software supports motif analysis and ORF search along with finding restriction cut sites on the nucleotide sequence.

The software has a built-in nucleotide-protein and protein-nucleotide sequence translator which can be used for designing degenerate primers for codons that code for multiple amino acid sequences. It is also understood that the primers designed by Primer Premier are effective and confirm to the design guidelines laid for designing primers for housekeeping genes with a high G+C%.[3]

The software also designs primers for flanking exons and introns in a gene, though there is no mention of it on the official Primer Premier page on the Premier Biosoft website.

The software calculates the hairpin structure stability and has been used to study its effect on PCR amplification.[4]

Competitors

There are many other software programs that design primers for the PCR reaction. Some of them are listed below:

  1. Geneious
  2. Primer3[5]
  3. DNASTAR's products such as SeqBuilder and PrimerSelect
  4. AlleleID (produced by the same company as Primer Premier)
  5. PrimerX (for site-directed mutagenesis)
  6. GenomePride[6]
  7. OLIGO

References
  1. Zhaohui S, Wenling Z, Bao Z, Rong S, Wenli M. Microarrays for the detection of HBV and HDV PMID 15479617
  2. Sensitivity, specificity and stability of the Tag-primer nested/multiplex PCR for malaria diagnosis Guo CK, Li XM, Li JH, Mao W, Lin Z, Du JF, Huang TY. PMID 18038781
  3. Guo YP, Huang Y.Design and validation of primers for housekeeping genes of streptomycetes PMID 18271268
  4. http://www.horizonpress.com/mbt/v/v1/11.pdf
  5. "Primer 3". primer3.sourceforge.net.
  6. Haas, Stefan A. "GenomePRIDE - PCR primer design / oligo design software". pride.molgen.mpg.de.
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