List of key tools for identifying and annotating ncRNAs in plants
| miRPlant | Identification of miRNAs from RNA-seq data An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275.https://sourceforge.net/projects/mirplant/ |
| miRanalyzer | Identification of miRNAs and analysis of RNA-seq data (2017)https://sourceforge.net/projects/mirplant/http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php |
| miRA | Identification of miRNAs in organisms without existing miRNA annotation or without a known related organism with well-characterized miRNAs Michael Huttner (2016)https://github.com/mhuttner/miRA |
| miRDeep-P | A modified miRDeep to predict plant miRNAs (2012) http://faculty.virginia.edu/lilab/miRDP/ |
| Semirna | Identification of miRNAs using target sequences http://www.bioinfocabd.upo.es/semirna/ |
| TAPIR | Prediction of miRNA targets, including target mimics http://bioinformatics.psb.ugent.be/webtools/tapir/ |
| psRNATarget | Prediction of miRNA targets, including reverse complementary matching and target site accessibility evaluation (2017) http://plantgrn.noble.org/psRNATarget/ |
| MicroPC | Identification of miRNAs and prediction of their targets from large-scale EST analysis (2009) http://www3a.biotec.or.th/micropc/index.html |
| C-mii | A software for Computational miRNA identification) Identification of miRNAs and prediction of their targets http://www3a.biotec.or.th/c-mii/ |
| MTide | Identification of miRNA − target interaction by combining modified miRDeep2 and CleaveLand4 (2014) Ming Chen’s Bioinformatics Group, Zhejiang University. http://bis.zju.edu.cn/MTide/ |
| BioVLAB-MMIA-NGS | (MMIA= miRNA mRNA Integrated Analysis) Integrated analysis of miRNAs and mRNAs using high-throughput sequencing data http://epigenomics.snu.ac.kr/biovlab_mmia_ngs/ |
| PhlyoCSF | Calculation of lncRNA coding potential using codon substitution frequency score https://github.com/mlin/PhyloCSF |
| CPC | Calculation of lncRNA coding potential using sequence features and support vector machine (2007-2015) http://cpc.cbi.pku.edu.cn/ |
| CNCI | Calculation of lncRNA coding potential by profiling adjoining nucleotide triplets https://github.com/www-bioinfo-org/CNCI |
| CPAT | (Coding Potential Assessment Tool) Calculation of lncRNA coding potential using a logistic regression model http://rna-cpat.sourceforge.net/ |
| DeepLNC | Prediction of lncRNAs using deep neural network https://bioserver.iiita.ac.in/deeplnc/index.php |
| iSeeRNA | Prediction of lncRNAs using support vector machine algorithm. CUHK (2014)http://137.189.133.71/iSeeRNA/ |
| RegRNA | Identification of regulatory RNA motifs http://regrna2.mbc.nctu.edu.tw/index.html |
| spongeScan | Identification of miRNA spongeshttp://spongescan.rc.ufl.edu/ |