Degenerate Primer Design Using Computational Tools Computational Molecular Biology

The polymerase chain reaction (PCR) is widely used to uncover new information about genes and genomes, but is limited in that it is highly dependent on the use of specific and sensitive primers to yield good results. Primers can target a specific, known sequence, but what is often more interesting is the use of degenerate primers to target unknown sequences. Degenerate primers are designed based on multiple known sequences for a gene family, and can be used to discover new homologs in other species. Here, I review three programs that focus on the design of degenerate primers to search for unknown genes: HYDEN, SCPrimer, and iCODEHOP. The algorithms, advantages, and limitations of each are discussed. Although HYDEN and SCPrimer are promising programs in terms of optimizing the degeneracy of each primer, CODEHOP is the most widespread in use (Chakravorty and Vigoreaux 2010; McMahon et al. 2002; Pereyra et al. 2010). This is likely due to its focus on biologically relevant constraints and ease of use in designing primers (Staheli et al. 2011).