Welcome to Rsite2
Rsite2 is a secondary structure based computational method to predict the functional sites of noncoding RNAs (ncRNAs), which represent a big class of RNA molecules that show critical regulatory functions in a variety of biological processes. Recently, as the number of ncRNAs increases greatly, the demand for identifying the functional sites of ncRNAs grows fast, whereas the available computational methods are limited.
For the above purpose, in a previous study, we developed a tertiary structure based method, Rsite. However, the application of Rsite is largely restricted because of limited RNA tertiary structures, hard to analyse and predict. Fortunately, we observed that ncRNA secondary structures and tertiary structures show significantly positive correlation. This makes it reasonable to replace tertiary structure with secondary structure, which is much more easily to obtain.
So we present here Rsite2. For the given ncRNA sequence, Rsite2 identifies as functional sites the nucleotides locating within the extreme points in the distance curve derived from the secondary structure predicted by RNAfold (Hofacker et al. 1994).
Dr. Qinghua Cui Department of Biomedical Informatics Peking University Health Science Center 38 Xueyuan Rd, Beijing 100191 China Email: cuiqinghua(at)hsc.pku.edu.cn