Primer Multiple Sequence Alignment and Design Tool

Primer Premier 5 integrates multiple sequence alignment (ClustalW) with primer design to facilitate the design of primers that can be used for cross species, pathogenic, or allele specific research. The primer design tool designs optimal primers for PCR, sequencing and hybridization quickly. Primers can be designed automatically or manually. With the automatic search, the program gradually relaxes the stringency of the search until the best possible primers available within the target sequence are found. The primers are located to optimize for T_m, GC%, GC clamping, 3-in end stability, and to minimize hairpins and dimers. For experimental designs requiring a finer degree of control, the manual search allows exact primer criteria to be set and all primers meeting the criteria are located. The resultant primers are ranked both individually and paired based on their priming efficiency. The selected primers or pairs can be ordered easily by printing the synthesis order form provided.

Many specialized primer design needs are addressed. Primers can be designed by back translating a protein sequence and locating primers with the region of lowest degeneracy. Multiplex/nested primer design ensures that no cross homologies exist between any primers in the primer pool when amplifying low copy targets. For long PCR primer design, it handles DNA sequences up to 50kb. Its ability to check for false priming against a directory of sequences results in reduced secondary banding. The product is available for Windows 95/98/NT/2000 and Power Macintosh Mac OS 9 or higher.

Premier Biosoft International, 3786 Corina Way, Palo Alto, CA 94303-4504. Tel: 650-856-2703; Fax: 650-843-1250.