General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Testing primers with MacVector 13

New to MacVector 13 is the ability to quickly test a pair of primers.

Previously to test a pair of primers with the Primer3 tool you needed to modify the expected product and reduce the stringency of all parameters so that your primers would be accepted.

Primer Design Primer3 and pBR322 nucl Map

Now when you enter a pair of primers into Design Primers (Primer3) the interface switches to a new testing mode, TEST PRIMER PAIRS. At this point all parameters are relaxed so that your primers are always accepted.

A new enhanced summary page then shows statistics about your primers.

PBR322 nucl Map

All reaction conditions are now shared. so if you change [dNTP] in one tool they are changed and used for all other tools to achieve consistency of results.

.. and don’t forget that since MacVector 12.6 all the tools in MacVector use the Santa Lucia algorithm for calculating melting temperature of the primers. This algorithm by John SantaLucia (PNAS 95:1460-1465, 1998) has become widely accepted as producing the most accurate values for the melting temperature of DNA.

This entry was posted in Releases, Tips and tagged , , . Bookmark the permalink. Both comments and trackbacks are currently closed.