prediction of novel microRNAs from deep sequencing data? - microRNA deep sequencing (Aug/02/2009 )

Hi there,

I have done illumina/solexa deep sequencing of rat total RNA +/- my drug of interest. I have some reads that align to known microRNAs, which is good. I also have some high intensity reads that align in areas with no known microRNAs. Presumably, some of these alignments harbor novel microRNAs. Does anyone know how to predict novel microRNAs from deep sequencing data? I have tried miRDeep and all of my positive controls failed, so that program isn't working for me. Does anyone know if there is a consensus site for Dicer cleavage of pre-miRNA? How can I go about doing this? All suggestions are welcome!

I don't know of any Dicer consensus sequence, so if you find a reference could you let me know? For testing if it's a miRNA though, you could put the expected pre- miRNA sequence into an RNA secondary structure tool, such as RNAfold, and see if it gives the expected hairpin with ~22nt stem.