# Comparison of Monkeypox and Wart DNA Sequences with Deep Learning Model
## 2 Material and Methods
### DNA-Mapping Methods  
In order for DNA sequences to be evaluated using artificial intelligence methods, the sequences must be converted into numerical expressions. DNA sequences consist of four bases. These bases are adenine (A), thymine (T), cytosine (C) and guanine (G). There are methods in the literature that can convert these bases into various numerical expressions. In this study, some of these methods were used and DNA sequences were mapped. In line with the study, five different methods were used: integer number representation, real number representation, atomic number representation, EIIP, and molecular mass. The integer-mapping method is widely used in DNA studies [18]. In this method, DNA bases are first listed alphabetically and after the sorting process, integer values are assigned to the bases. In this direction, the value is 1 for the A base, 2 for the C base, 3 for the G base, and 4 for the T base. For example, a DNA sequence S(n) = [ACTGCTAGC] is mapped as C(n) = [124324132] with the integer number representation method. In the real-number-mapping technique, the bases are assigned values of \(-\)1.5 and 0.5. These values differ for bases. In this method, the A base takes the value \(-\)1.5, while the T base takes the value 1.5. In addition, the C base is expressed with the value of 0.5, while the G base is converted into a numerical expression with the value \(-\)0.5. The integer and real-number-mapping methods are frequently used in studies carried out with artificial intelligence. The biggest reason for this situation is that the deviations in these methods are symmetrical [19; 20]. For example, a DNA sequence of S(n) = [ACTGCTAGC] is mapped as C(n) = [\(-\)1.5 0.5 1.5 \(-\)0.5 0.5 1.5 \(-\)1.5 \(-\)0.5 0.5 using the real mapping method. In the molecular mass DNA-mapping method, the numerical values of the bases are determined  
\begin{table}
\begin{tabular}{c c c c} \hline \hline
**Virus Type** & **Num. of Genomes** & **Sequence Length** & **Num. of Features** \\ \hline MPV & 55 & 198,740 & 10,930,700 \\ \hline HPV & 55 & 198,740 & 10,930,700 \\ \hline \hline \end{tabular}
\end{table}
Table 1: Information about the data set in the study.  
based on their molecular masses [21; 22]. In this method, A = 134, C = 110, G = 150, and T = 125 values are used. For example, a DNA sequence S(n) = [ACTGCTAGC] is converted into a numerical expression such as C(n) = [134 110 125 150 110 125 134 150 110] by the molecular mass DNA-mapping method. Integer number, real number, and molecular mass mapping methods are evaluated in the category of fixed mapping methods. The atomic number and EIIP methods are the leading physicochemical-based mapping methods. The atomic numbers of the bases are considered in the atomic mapping method [23]. In line with this method, the A base takes the value 70 and the G base takes the value 78. Moreover, the C base is denoted with the value 58, while the T base is expressed by the value 66. For example, a DNA sequence given as S(n) = [ACTGCTAGC] is converted into numerical expressions such as C(n) = [70 58 66 78 58 66 70 78 58] by the atomic number mapping method. In the EIIP DNA-mapping method, each nucleotide found in the sequence is matched with the half-valence numbers in the EIIP representation [24]. In this method, the A base takes the value 0.1260, the G base takes the value 0.0806, the C base takes the value 0.1340, and the T base takes the value 0.1335. For example, a DNA sequence given as S(n) = [ACTGCTAGC] is converted into numerical expressions such as C(n) = [0.1260 0.1340 0.1335 0.0806 0.1340 0.1335 0.1260 0.0806 0.1340] by the EIIP DNA-mapping method.