This document contains advice on the factors that students should consider when designing PCR primers to resolve gaps and low quality regions. The document also includes the specific search parameters students should use to minimize the chance of off-target priming when designing PCR primers.
Students use grasshoppers collected from glades in the Missouri Ozarks to generate and analyze sequence data to determine if the grasshopper populations are becoming fragmented due to the suppression of forest fires. Sequence data are provided here so students who do not have access to grasshoppers can still perform the sequence analysis portion of the lab.
Students use two different protocols, one based on sequence analysis and one based on biochemistry, to determine the identity of an unknown bacterial strain.