Designing degenerate PCR primers

Selecting Degenerate Multiplex PCR Primers

Single Nucleotide Polymorphism (SNP) Genotyping is an important molecular genetics technique in the early stages of producing results that will be useful in the medical field. One of the proposed methods for performing SNP Genotyping requires amplifying regions of DNA surrounding a large number of SNP loci. In order to automate a portion of this method and make the use of SNP Genotyping more wi...

Designing PCR Primers Painlessly†

Designing PCR primers on the Web.

MAD-DPD: designing highly degenerate primers with maximum amplification specificity.

This work introduces minimum accumulative degeneracy, a variant of the degenerate primer design problem, which is particularly useful when a large number of sequences are to be covered by a set of restricted number of primers. A primer set, which is designed on a minimum accumulative degeneracy basis, especially helps to reduce nonspecific PCR amplification of undesired DNA fragments, as fewer ...

Amplicon: software for designing PCR primers on aligned DNA sequences

SUMMARY Amplicon is a program for designing PCR primers on aligned groups of DNA sequences. The most important application for Amplicon is the design of 'group-specific' PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. AVAILABILITY Amplicon is freely available as a script that will run on any platform wi...