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== External links ==
* [http://cm.jefferson.edu/CLIPSim-MC/ CLIPSim-MC]: CLIPSim-MC is a tool that uses CLIP-seq data to find [[miRNA]]/MRE pairings using a Monte-Carlo-based approach.<ref>{{citation |journal=Scientific Reports |author1=Peter M. Clark |author2=Phillipe Loher |author3=Kevin Quann |author4=Jonathan Brody |author5=Eric R. Londin |author6=Isidore Rigoutsos |title=Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types |volume=4 |issue=5947 |pages=5947 |year=2014 |pmid=25103560 |doi=10.1038/srep05947 |pmc=4894423|bibcode=2014NatSR...4E5947C }}</ref>
* [https://web.archive.org/web/20110222111721/http://starbase.sysu.edu.cn/ starBase database]: a database for exploring miRNA-mRNA, miRNA-[[lncRNA]], miRNA-[[sncRNA]], miRNA-[[circRNA]], miRNA-[[pseudogene]], protein-[[lncRNA]], '''[[protein-RNA]]''' interactions and [[ceRNA]] networks from '''HITS-CLIP''' ('''[[CLIP-Seq]]''', '''PAR-CLIP''', '''[[iCLIP]]''', '''CLASH''') data, and '''[http://www.targetscan.org TargetScan]'''<ref>{{Cite journal|title = Predicting effective microRNA target sites in mammalian mRNAs
* [http://www.clipz.unibas.ch/ clipz]: a pipeline to analyze short RNA reads from HITS-CLIP experiments.
* [http://qbrc.swmed.edu/software/ dCLIP]: dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments.
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