imiRTP: a toolkit to genome-scale identification miRNA-target interactions in Arabidopsis thaliana

Jiandong Ding, Shusi Yu, Uwe Ohler, Jihong Guan and Shuigeng Zhou.

      Here, we present the first intergrated miRNA-target interaction (MTI) prediction and analysis toolkit -- imiRTP, for Arabidopsis thaliana microRNAs. By far, four popular tools(psRNATarget, TAPIR, UEA toolkit, WMD3) and four efficent fileters (multi-method, multiplicity, accessibility and Degradome-seq support) were intergrated. In futhur, more target prediction tools and filters will be considered.

      Currently the imiRTP program (version 1.0) is available only for the windows (Vista/Windows 7) platform. Microsoft .NET Framework 3.5 or higher version may be required.

• ImiRTP is develeped for searching qualified Arabidopsis MTIs. Both user-submitted miRNA and transcript sequences are accepted.
• Install and execute the miRFam as follows:

• Hint: make sure your computer can connect the internet when you are runing imiRTP.

• 142 experimentally validated MTIs: Supplemental Dataset One
• 25,688 Degradome sequencing validated MTIs: PARE-CLIP data
• all supplement tables: supplemental tables

Other useful links:

• miRBase: http://www.mirbase.org/
• miRTarbase: http://mirtarbase.mbc.nctu.edu.tw/
• starbase: http://starbase.sysu.edu.cn/
• psRNATarget: http://plantgrn.noble.org/psRNATarget/
• TAPIR: http://bioinformatics.psb.ugent.be/webtools/tapir/
• UEA toolkit: http://srna-tools.cmp.uea.ac.uk/plant/cgi-bin/srna-tools.cgi
• WMD3: http://wmd3.weigelworld.org/cgi-bin/webapp.cgi?page=TargetSearch;project=stdwmd