Список инструментов для идентификации ncRNAs

Список основных инструментов для идентификации и аннотации ncRNAs у растений

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 sponges

http://spongescan.rc.ufl.edu/