Could I use transcriptomics data to look for pri-miRNA sequence - (Mar/26/2009 )
I am working on discovering new miRNA in plants now. I have some miRNA candidates and transcriptomics data. I am wondering whether I could blast miRNA sequence against transcriptomics data to find the pri-miRNA sequence and predict second structure according to these sequence information.
So your assumption is that most if not all miRNA should be expressed and be captured in transcriptome. I don't know how plant microRNA differ from mammalian, I know mammalian microRNAs are too small to be on the radar screen of transcriptome. Alhtough precursor miRs are bigger than mature ones, they are short lived and won't appear in transcriptome either.
Many plant pre-miRNAs are found in EST libraries, so you can try to blast your miRNA candidates and look for secondary structures.