Untranslated region in RNA; Internal ribosome entry site (IRES) is crucial to exploring and deciphering the initiation mechanism of translation and replication of the virus, where IRES contains some conserved motifs existing in the function domain of IRES which are essential for IRES activity to start its. The existing RNA structure prediction programs are not sufficient in prediction IRES structure, because IRES have special nature differ from other RNA sequences. The objective of this paper is : Provide more reliability in the secondary structure level for RNA which have a special nature like function domain of IRES called; Apical. The proposed approach uses rule-based criteria, which use some predetermined parameters as energy, conserved motifs and loops of the predicted structure. The proposed approach applied on 50 sequences and have low error rate and up to 68 % accuracy at the first iteration and 100 % accuracy after the second iteration |
