# A Method for Degenerate Primer Design Based on Artificial Bee Colony Algorithm
## 4 Experimental Results
### Comparison with Related Algorithms
#### 4.2.2 Analysis and Comparison on the Basis of Descriptive Statistics  
From 100 groups of DNA template combinations, the 500 bps DNA template and the 600 bps DNA template are selected as the test cases. The specific experimental data (such as primer pair composition, degeneracy, coverage, primer length, GC content, specificity, and other evaluation indexes) of the DPD-HABC algorithm, Primer 5, and Oligo 7 are shown in Table 2.  
Figure 5: The adjustment of parameter \(\varphi\). Figure 6: Convergence graphs for DPD. From Tables 2 and 3, it can be seen that, from the perspective of degeneracy, the degeneracy of the DPD-HABC algorithm based on the hybrid artificial bee colony optimization model for degenerate primer design is 3072 and 1536, respectively; values which are significantly lower than the results for the solutions obtained when using the software programs Primer 5 and Oligo 7. With respect to coverage, the coverage of the DPD-HABC algorithm based on a hybrid artificial bee colony optimization model for degenerate primer design is 30, which is significantly higher than that of Primer 5 and Oligo 7. In addition, the primer pairs solved using the DPD-HABC algorithm are specific compared with the other two software programs, and the quality of the primer pairs obtained using the DPD-HABC algorithm are inseparable from the processing of search space. The specific experimental data of the DPD-HABC algorithm on two DNA template sequences of 100 bps and 200 bps are shown in Table 4. \begin{table}
\begin{tabular}{c c c c} \hline \hline  & **DPD-HABC** & **Primer 5** & **Oligo 7** \\ \hline  & T[AC][AT][AGC]A & [AT] A [AT][AGC][CA] & [AT][AC][AT]A[CA] \\ Forward primer (5\({}^{\prime}\)-3\({}^{\prime}\)) & [AG]A[GT]GG & GC[AT][GT][GC] & [AG][GC]A[GT]G \\  & G[TC][TG][TC][GT] & [TG][TTC][TG]C & [CTG]G[TC][TTC] \\  & [AC]AGG(TC) & T[AC][AT]GG & T[AC]AG[AG] \\  & TAC[GC][AT]C & [AT][AC][GC][ATC] & [AG] A CG[AT] \\ Reverse primer (5\({}^{\prime}\)-3\({}^{\prime}\)) & [AT][GC][TC]C & [GA][AT][GC]C & [GAT]AG[TC][CG] \\  & [ AG ][AT][GC][TG] & [TG][GAT][AA]C & TG[AT]A[AC] \\  & [AT][AT]TC[CT] & [CG][AT][AT]TTC & & \\ Degeneracy (F/R) & 3072/3072 & 6144/12,288 & 6144/4608 \\ \multicolumn{2}{c}{Converge (F/R)} & 30 & 20 & 25 \\ \multicolumn{2}{c}{Primer length (F/R)} & 20/20 & 20/20 & 20/20 \\ \multicolumn{2}{c}{Melting temperature} & 57/55 & 60/62 & 61/63 \\ \multicolumn{2}{c}{(F/R) (\({}^{\circ}\)C)} & 2 & 2 & 2 \\ \multicolumn{2}{c}{Temperature difference (\({}^{\circ}\)C)} & \multicolumn{1}{c}{52} & 53 & 54 \\ \multicolumn{2}{c}{GC-clamp (F)} & \multicolumn{1}{c}{CG} & \multicolumn{1}{c}{CG} & \multicolumn{1}{c}{GG} \\ \multicolumn{2}{c}{GC-clamp (F)} & \multicolumn{1}{c}{CG} & \multicolumn{1}{c}{CG} & \multicolumn{1}{c}{GG} \\ \multicolumn{2}{c}{GC-clamp (R)} & \multicolumn{1}{c}{G} & \multicolumn{1}{c}{CG} & \multicolumn{1}{c}{CG} \\ \multicolumn{2}{c}{Self-annealing} & \multicolumn{1}{c}{No} & \multicolumn{1}{c}{No} & \multicolumn{1}{c}{No} \\ \multicolumn{2}{c}{Pair-annealing} & \multicolumn{1}{c}{No} & \multicolumn{1}{c}{No} & \multicolumn{1}{c}{No} \\ specificity & \multicolumn{1}{c}{Yes} & \multicolumn{1}{c}{No} & \multicolumn{1}{c}{No} \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Comparison of three methods on 500 bps DNA template.