I want to predict miRNA targets for some mRNAs. Are there any prediction tools that allow mRNA sequences as input and then provide the targeting miRNAs? I know there are several miRNA target prediction tools out there but I always only find options to put in gene IDs or miRNA IDs and not sequences. I also could provide structural information about the mRNA for target site accessibility and so on but I do not have gene IDs... Is there a specific tool that provides this option? Thanks!
For most of these tools you can run in two ways. You can either query pre-computed sets of targets for analysed species or you can run the algorithm yourself to generate predictions for sequences that havn't already been analysed.
Often the way this works is that the the website provides access precomputed targets (e.g. microrna.org or targetscan.org), and if you want to analyse sequence, rather than using the pre-computed values, you have to download the program and run it yourself on a local machine. Some of these programs are easy to run (e.g. miRanda), some are less easy (e.g. TargetScan).
PITA is the only tool I know of that allows you to input an arbitrary mRNA sequence on the website. But then it requires to select a spieces, I guess so that it can get the list of miRNAs.