RNA-Seq: distinguish lncRNA of smRNA precursors

[int11ap1]

Hi everybody,

I have some data from RNA-seq. This data does NOT come from a library of small RNAs, but comes from a library of mRNAs and total RNA. From this data, I perform an alignment with TopHat, followed by cufflinks and annotation of the genes. After this point, I have a pipeline that extracts the lncRNAs from the other RNAs.

Once I have the lncRNAs, how could I differentiate the precursors of small RNAs from the "real" lncRNAs? I know that the vast majority of publications performs a BLAST against the existing database of miRNAs, and I have that in mind. However, I would like to ask if there exists another method, software, etc. that takes into account the secondary structure of the lncRNAs in order to say: OK, this might be a precursor of any small RNA (miRNA, siRNA, shRNA,...).

Do you have some suggestions?

Thanks in advance.

PD: I am working with plant transcriptome.

[TiborNagy]

UEA has a strategy to find novel miRNA from sequencing data.

Another interesting method is iMir, however I have not tested yet.

[int11ap1]

Thank you for the reply, TiborNagy. Nevertheless, the packages you suggest work only with small RNA-seq data! What if my library is a cDNA library?

The aim is to find pre-miRNAs from my annotated lncRNAs.