21U-RNAs are members of a diverse class of small RNAs that are expressed in Caenorhabditis elegans. They are derived from thousands of loci spread across chromosome IV and are generated in a manner that is independent of components of the RNAi pathway. Their common feature is the presence of an ustream motif that is largely sufficient to predict their identities and whose agreement with their consensus sequence correlates directly with the magnitude of their expression.
Here, I provide a computational tool for scoring the 21U-RNA-associated upstream motifs. This tool has been used to predict 21U-RNAs from genomic sequence and to classify 21U-RNAs from high-throughput small-RNA sequence datasets. It is provided as a module that extends the python programming language.
Software and documentation written by J. Graham Ruby.