Primer Premier 6.0

Primer Premier is the most comprehensive software to design and analyze PCR primers.
Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor thermodynamic algorithm. Primers are screened for secondary structures, dimers, hairpins, homologies and physical properties before reporting the best ones for your sequence, in ranked order. Equipped with a handy calculator, you can easily manipulate sequences and analyze the results of your primer design.

Load the gene of interest from NCBI, select a search range, sit back and let Primer Premier pick the best possible primers for you.
Primer Design for SNP Genotyping Assays

With Primer Premier, you can load sequences from dbSNP and have the primers designed flanking the SNP selected. Hundreds of unpublished SNPs can also be loaded by specifying them as variation features in standard GenBank/dbSNP files. After specifying the SNPs, primers can be designed to amplify them for detection using a probe-based chemistry.
Multiplex Primer Design

For a multiplex experiment, Primer Premier enables you to design multiplex primers by launching a primer search in batch mode and then checking the cross reactivity of the primers designed. Primer Premier checks for all the possible reactivity and displays the most stable structure formed by each oligo. This functionality reduces false priming and ensures a strong signal strength.
Automatic Homology & Template Structure Avoidance

Primer Premier automatically interprets the BLAST search results and avoids those regions to design primers that have significant cross homologies with the database. These homologous regions are highlighted in the sequence view and are avoided during primer search.

Primer extension may be hindered due to the presence of template structures at extension temperature. To avoid all such regions, where the template may fold upon itself, the program utilizes a proprietary algorithm to check for possible secondary structures within the template at a folding temperature you specify. The regions involved in the formation of a secondary structure are underlined in the sequence view and are avoided while designing primers.

Avoiding homologous regions makes the oligos highly specific and avoiding template structures improves the efficiency of the designed primers.