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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.

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 Hundreds of unpublished SNPs can also be loaded by specifying them as variation features in standard GenBank/dbSNP files.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.

FEATURES

PCR primer design- design primer pairs for PCR and multiplex experiments.
Cross species- Amplify sequences from multiple species.
Pathogenic detection- Locate oligos in highly conserved regions.
Allele specific- Exclusively amplify a single member of a set of related sequences.
Degenerate- Start with an amino acid sequence, reverse translate and design oligos in regions of low degeneracy automatically.
Nested/multiplex- Checking homology among multiple candidate oligos.
Restriction enzyme and motif analysis- Select from the database of over 800 enzymes and 200 common motifs.
Clustal W alignments- Load the aligned sequences after performing ClustalW alignment using any resource, including EBI.
Multiple sequence alignment- Use the popular Clustal W algorithm to align sequences from your desktop (available in Windows version only).
Algorithm- Calculates Tm using Breslauer values.
Long PCR- Handles sequences up to 50 KB.