miRNA identification in plants using smallRNA deep SEQ data

[PRJ]

I am trying to identify miRNAs (novel and conserved) in a plant species using small RNA deep sequencing and a draft genome (~8x coverage). The only problem is that we are not able to release the genome publicly yet. I have seen that there are online programs that have published genomes uploaded - miRcat, miRanalyzer, etc.

I would like to run a program on my computer to identify miRNAs based on sRNA SEQ and a draft genome. I know there is miRDeep but this seems to be specifically for animal miRNAs which have a more constrained hairpin structure.

Does anyone know of any programs that I could run on my own computer, not on the internet, to identify miRNAs using my sRNA SEQ and draft genome?

Does anybody have any other ideas? - Thanks

[Latifa77]

Hi,
How did you solve your problem? Does anyone who is working with miRNAs in plant and deep sequencing ??? Please.

[Blahah404]

The seqmentSeq R package is designed for small RNA discovery in plants.

Paper is here: http://bioinformatics.oxfordjournals...28/4/457.short

[Latifa77]

Hi Blahah404,
Thanks for you answer. I see that seqmentSeqR is for siRNAs, but I woukd like a program to identify miRNAs.

[Blahah404]

Whoops, sorry, misread the question.

Two options that I know of:

mirDeep-P
ShortStack