Algorithms for the Multiple Degenerate Primer Selection Problem

The multiplex polymerase chain reaction (MP-PCR) is a quick and an inexpensive technique in molecular biology for amplifying multiple DNA loci in a single Polymerase Chain Reaction (PCR). One of the criteria to achieve highly specific reaction products is to keep the concentration of the amplification primers low. In research, the dilemma associated with primer minimization for MP-PCR reactions has been formulated as the Multiple Degenerate Primer Selection Problem (MDPSP). MDPSP is related to the earlier Degenerate Primer Design (DPD) problem that has proven to be NP-complete. This paper formulates a new, so far, unexplored variant, the Multiple Degenerate Primer Selection Problem with Errors (MDPSPE) and introduces algorithm DPS-HDE for solving this new version. Implementing DPS-HDE on randomly generated datasets greatly reduced the number of primers in the output and the time of execution. Furthermore, we also introduce a new exact algorithm, DPS-HDR for solving the earlier MDPSP and compare the algorithm’s performance on randomly generated datasets with DPS-HD, thus far the most efficient algorithm for solving MDPSP introduced by Balla et al. in [2]. DPS-HDR executed slower than DPSHD, however, with the same quality of output.