FindTar3 Online Prediction
FindTar3 predicts miRNA targets based on the common criteria, including seed-pairing, free energy of miRNA:target duplex, and proper dynamic programming score. However, the importance of partial complementarity between miRNAs and their targets is the special concern in FindTar3, which is necessary to avoid microRNA target induced instability of microRNAs. The partial complementarity of miRNA:target duplex is presented as central loop score in FindTar3.
FindTar3 provides pre-calculated genome-wide miRNA target database in FindTarBase webpage for the comprehensive view of human, mouse and rat, or customized your miRNA and/or mRNA sequences for online target prediction. The miRNA sequence of database is retrieved from miRBase release version 16 and the Refseq gene sequence is retrieved from UCSC Genome Bioinformatics. (Last update in Nov 18, 2010)
References:
The Effect of Central Loops in miRNA:MRE Duplexes on the Efficiency of miRNA-mediated Gene Regulation- Wenbin Ye, Qing Lv, Chung-Kwun Amy Wong, Sean Wu, Chao Fu, Zhong Hua, Guoping Cai, Guoxi Li, Burton B. Yang, Yaou Zhang. PLoS One,3:e1719 (2008)[full text]
Target RNA-Directed Trimming and Tailing of Small Silencing RNAs- Stefan L. Ameres, michael D. Horwich, Jui-Hung Hung, Jia Xu, Megha Ghildiyal, Zhiping Weng, Phillip D. Zamore.Science,328:1534(2010)[full text]
