Primer design

Primerdesign is performed manually with help of special software for single oligonucleotides and automatically for polishing/finishing steps of newly assembled (areas of) genomes.

A lot of different criteria are included in the final design as: Overall GC content, GC content within the 3' and 5' primer ends, homopolymer stretches, secondary structures, selfcomplementary and helpfull bases at the 3' end and following the primer. All primers are optimized for binding with maximal specifity.

The anealing temperature of oligonucleotide primers can be calculated here.