February 15, 2014 (Vol. 34, No. 4)
Strong Points: Easy to use, adjustable parameters
Weak Points: Need to register for free account to access
NetPrimer is not one of those primer tools that will do all of the work for you and design the primers; however, if you have primer sequences, NetPrimer has the analytical power to tell you how good your primers are. Simply enter a sequence into the NetPrimer Java applet and hit “analyze” to identify any palindromic, repeat, or run sequences within your primer, and to reveal whether your primer will form hairpins or dimers. NetPrimer will also return a number of calculated values for the inputted sequence, including melting temperature, GC composition, and various energy values. These values are calculated from a set of default parameters (ion concentrations, temperature, etc.) that can be modified by the user. The NetPrimer tool allows users to enter both a sense and antisense primer sequence to also assess interprimer interactions. Users can choose to enter names and descriptions for their primer sequences, which is useful given that users can print the resulting analyses.