In the present in silico viral genetics study, a mathematical method was developed for the comparison of RNA sequences The mathematical method used was to explore component similarities and patch them together with a modern geometric statistical projection method called multidimensional scaling (MDS) The comparison looked into similarities between ≈300 nucleotides (NT) of 7SL RNA and size ≈300 NT sub-sequences of SARS-CoV-2 Spike mRNA RN7SL2 and RN7SL3 were also compared with SARS-CoV-2 Spike mRNA In the component comparison, use was made of a He Hamiltonian model for the approximation of the density distribution of the outer two electrons This was considered a basic ingredient of similarity Improvements can be implemented later on With MDS it is possible to blend theoretical with experimentally obtained characteristics of components Furthermore, complementarity was employed to derive a numerical representation of the formation of RNA knots With the use of crystallographic and electron microscopic coordinate data sets, we aimed to study a more geometric structure of comparing RNA with RNA and RNA with SRP9/14 protein We found reason to believe that subsequences of the S2 SARS-CoV-2 Spike mRNA around position NT = 3620, can possibly behave similar to 7SLRNA The latter can form “parasitic” Alu DNA The hypothesis is drawn that under conditions where e g broken DNA occurs and RNA dependent DNA polymerase is present these RNA subsequences can, because of similar affinity to SRP9/14, be transformed into transposons and become a DNA parasite
Approximative He Hamiltonian in descriptive multidimensional scaling statistics of RNA contained information with application to SARS-CoV-2 Spike mRNA and 7SLRNA, RN7SL2 and RN7SL3