miRNA target package/program

[Nnogueira]

Hi,

I was able to obtain a list of miRNAs from my RNA-seq data, but now I would like to analyze potential targets.

Is there any software or bioconductor's package that allows me to identify potential targets?

Thanks in advance!

[sali]

Hi,
I am trying to predicate LncRNA from aPlant species. I have sequenced total RNA and then proceed to do the de novo assembly to get the transcriptome. Any idea about how to predicate the LncRNA target without reference genome?
searching for the CPC software and phyloCSF but how can perform them from the basic I don't really know? Thank you so much!

[liweixie]

You can use certain spicy whom genome as reference. Those RNA-seq mapped back to the region other than protein coding RNA also can plus the rRNA and tRNA annotation to give higher output