Restriction enzyme and motif analysis- Select from the database of over 800 enzymes and 200 common motifs.Ĭlustal W alignments- Load the aligned sequences after performing ClustalW alignment using any resource, including EBI. Nested/multiplex- Checking homology among multiple candidate oligos. Pathogenic detection- Locate oligos in highly conserved regions.Īllele specific- Exclusively amplify a single member of a set of related sequences.ĭegenerate- Start with an amino acid sequence, reverse translate and design oligos in regions of low degeneracy automatically. PCR primer design- design primer pairs for PCR and multiplex experiments.Ĭross species- Amplify sequences from multiple species. After specifying the SNPs, primers can be designed to amplify them for detection using a probe-based chemistry. Hundreds of unpublished SNPs can also be loaded by specifying them as variation features in standard GenBank/dbSNP files. With Primer Premier, you can load sequences from dbSNP and have the primers designed flanking the SNP selected. Equipped with a handy calculator, you can easily manipulate sequences and analyze the results of your primer design. Primers are screened for secondary structures, dimers, hairpins, homologies and physical properties before reporting the best ones for your sequence, in ranked order. 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. Primer Premier is the most comprehensive software to design and analyze PCR primers.
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