| siExplorer is an algorithm developed for designing effective siRNAs on the basis of a statistical examination of RNAi activities and sequence characteristics. In this algorithm, total base composition and base-specificity at every third position of siRNA are mainly considered for calculating the prediction score.
Consensus sequence of active siRNA is 5'-NNAANAANNUNAANAWNAA-3', where A/U at positions 3n+1 have positive effect on the activity.
To use siExplorer, enter a particular sequence or an accession number of a gene in the text area and check the radio button. When entering a target sequence, letters other than A, U, T, G, C, N are not allowed. An accession number must represent valid RNA or DNA sequence. Search of siRNA sequence will be started by submitting these data. Then, top 10, 20 or 50 siRNA sequences will be displayed. siRNA sequences obtained by this algorithm can be used only for academic research purposes. Diagnostic, therapeutic or other commercial uses are prohibited. Publication: "Specific residues at every third position of siRNA shape its efficient RNAi activity." T. Katoh and T. Suzuki. Nucleic Acids Res. 2007 Jan 26. Credits: siExplorer is developed by T. Katoh and T. Suzuki, Dept. of Chem. and Biotech., Grad. School of Engineering, Univ. of Tokyo. Copyright (c)2006. |