The blast results are then automatically analyzed to avoid primer pairs that can cause amplification of targets other than the input template. It uses Primer3 to design PCR primers and then submits them to BLAST search against user-selected database. Primer-BLAST was developed at NCBI to help users make primers that are specific to the input PCR template. The ePCR tool provides fast detection of mispriming sites and alternative PCR products in cDNA libraries and native or bisulfite-treated genomes. 35(Web Server issue):W71-W74)īiSearch Primer Design and Search Tool - this is a useful tool for primer-design for any DNA template and especially for bisulfite-treated genomes. Primer3Plus - a new improved web interface to the popular Primer3 primer design program ( Reference: A. GeneFisher - Interactive PCR Primer Design (Universitat Bielefeld, Germany) - a very good site allowing great control over primer design. Primer3: – This site has a very powerful PCR primer design program permitting one considerable control over the nature of the primers, including size of product desired, primer size and Tm range, and presence/absence of a 3’-GC clamp.
There are several excellent sites for designing PCR primers: Online Analysis Tools - PCR DESIGN PCR PRIMERSīACKGROUND INFORMATION: For sites describing PCR theory, as well as companies marketing PCR products you might want to begin by visiting Highveld.
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