[17][21][22][23][24] [27][28] webserver The single sequence methods mentioned above have a difficult job detecting a small sample of reasonable secondary structures from a large space of possible structures.
A good way to reduce the size of the space is to use evolutionary approaches.
For example, miRNAs regulate protein coding gene expression by binding to 3' UTRs, small nucleolar RNAs guide post-transcriptional modifications by binding to rRNA, U4 spliceosomal RNA and U6 spliceosomal RNA bind to each other forming part of the spliceosome and many small bacterial RNAs regulate gene expression by antisense interactions E.g. GcvB, OxyS and RyhB.
MicroRNAs regulate protein coding gene expression by binding to 3' UTRs, there are tools specifically designed for predicting these interactions.
For an evaluation of target prediction methods on high-throughput experimental data see (Baek et al., Nature 2008),[125] (Alexiou et al., Bioinformatics 2009),[126] or (Ritchie et al., Nature Methods 2009)[127] sourcecode