February 1, 2009 (Vol. 29, No. 3)
Strong Points: Useful calculations
Weak Points: Nothing significant
Premier Biosoft is a long-time molecular biology software developer that has specialized in interesting niche products. Many of them relate to PCR and primers, and they are available for purchase. It is rare, therefore, to find a developer like Premier Biosoft putting something it could easily sell online, free for all to use, but that is exactly what they did with NetPrimer. As the title states, NetPrimer is a tool for researchers to determine hybridization-related parameters for primers they hope to use. The program takes a user’s input sequence in the 5´–3´ direction and, at the click of a button, it calculates a rating of fitness for the primer, melting temperature, molecular weight, %GC, nmol per A260, and the energy of stability as a hairpin, as a dimer, and as a palindrome. The program will also identify any repeats in the sequence. While NetPrimer does not allow one to design primers, it is a handy little tool for analyzing them for problems.