The PCR primer design tool in the BIONUMERICS software searches for optimal primers or primer combinations for the most diverse experiment setups by taking into account a large number of experimental parameters. The user can specify various primer properties such as preferential length and melting temperature, %GC boundaries, maximal degeneracy, etc. Forward and reverse primers and PCR combinations can be sorted and selected according to different parameters (position, melting temperature, length, degeneracy, %GC...). Selected primer pairs can be stored in the oligonucleotide database.
![PCR primer design settings](/sites/default/files/img/Primer-design.png)
Primer design in the Multiple alignment window allows you to identify primer pairs that discriminate between defined groups of sequences, e.g. for application in highly specific PCR detection assays.