Thesis (Ph.D.) - Cairo University - Faculty of Computers and Information - Department of Computer Science

The lack of vaccines and drugs for viruses becomes a big challenge in the recent years, especially with the big variety of families and serotypes for each virus. This problem appears clearly with RNA viruses; because the big mutation and instability nature of this type of viruses, which prevent from the long life effect of the vaccines, so a lot of researches, have been conducted to overcome this problem whether at life cycle, genome sequencing, second and tertiary structure level. One of the viruses which affects directly on the animal health and its life at all and also effect on the economics of the world is foot-and-mouth disease virus (FMDV). Sequence of FMDV virus as other RNA viruses is divided into two main regions or parts; translated regions or coded regions and un-translated regions (UTR), the latter one called 2internal ribosome entry sites3 (IRES). Although UTR is un-coded region (don{u2019}t replicated to be a part in protein composition) but it is very important part in the virus life cycle; because the replication of the virus start from it. The biochemical studies have proven that; some domains in the genome have importance more than other regions, because it contain the function parts of those regions. Apical domain in internal ribosome entry site (IRES) of foot and mouth disease virus (FMDV) is one of these domains. The deep understanding to the nature of the virus affects positively in solving the addressed problem, since the data in the biology filed is so huge and still growing where the data is pillar of any research. This research tries to overcome some of FMDV challenges like the very fast mutation of the virus which need analysis and observations on a large scale to prevent the continual evolution of the virus

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