pRuNA

RNA Sequence

RNA Secondary Structure

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Summary

pRuNA aims to identify all potential regulatory ncRNAs that can establish stable joint structures with a query mRNA. An important component of pRuNA is a sequence filter which eliminates a significant fraction of the available ncRNA collection and retains only the most likely ncRNA candidates for forming a stable joint structure with the query mRNA. We note that the majority of regulatory ncRNAs are only partially complementary to their target mRNA sequences. Typically these RNAs contain at least two short (5-7 nt) motifs on their loop structures that are complementary to the specific single stranded locations in the target RNAs. Thus pRuNA first identifies all pairs of 5-mer motifs from the ncRNA loop sequences that are complementary to a pair of 5-mer motifs in the loop sequences of the query mRNA.

Input and Output

pRuNA asks for a query mRNA sequence as well as its corresponding secondary structure in parenthesis format. It returns a list of possible regulating ncRNAs available through the Rfam database.