As some popular ones like targetscan demand miRNA ids, means it can not be used for novel ones. Further as the number of miRNAs is quite high (nearly 400), we need a software capable of handling batch queries.
miRanda is capable of doing this if you download it and use the command line version instead of using the website.
http://www.microrna.org/microrna/getDownloads.do
Miranda and RNAhybrid (Offline), are the best software's for target prediction of list of miRNAs.
I would say TargetScanS it is really a good tool with high citation and ease of use.
thanks to all. Miranda is working with custom list but I find targetScanS demanding miRNA ids so couldn't use it for custom designed predictions
You may try also mirWalk, which integrates different prediction tools and predicted/validated mirnas.
Hello,
I would recommend mirWalk. It's a really good tool.
Good luck.
Venk
Can any one help me to understand miRdeep cut of score for selection of novel miRNAs
Check out http://www.nature.com/natureevents/science/events/47533-microRNA_Analysis_Using_Next_Generation_Sequencing
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