miRNA annotation tools for plants and animals

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miRNAannotation tools for plants and animals

Tools	Category	Organism	ML Method	Publication Span	Current Version	Aviailability	Reference
SUmirFind/SUmirFold	H	P	–	2012	–	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398953/bin/pone.0040859.s003.pdf	https://www.frontiersin.org/articles/10.3389/fpls.2016.02058/full
MIReNA	H & I	A, P	–	2010	–	http://www.lcqb.upmc.fr/mirena/index.html	http://dx.doi.org/10.1093/bioinformatics/btq329
miRDeep-P	I	P	–	2011	v1.3	https://sourceforge.net/projects/mirdp	https://academic.oup.com/bioinformatics/article/27/18/2614/181153
miRDeep-P2	I	P	–	2019	v1.1.4	https://sourceforge.net/projects/mirdp2	http://dx.doi.org/10.1093/bioinformatics/bty972
miRNAFold	I	A, P	–	2012–2016	–	http://evryrna.ibisc.univ-evry.fr/miRNAFold	http://www.ncbi.nlm.nih.gov/pubmed/27242364
miRPlant	I	P	–	2013	v0.1	https://sourceforge.net/projects/mirplant/	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-275
miR-PREFeR	I	P	–	2014		https://github.com/hangelwen/miR-PREFeR	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0798-3
mirinho	I	A, P	–	2015	–2015	http://mirinho.gforge.inria.fr/	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0594-0
miRA	I	P	–	2015	v1.2.0	https://github.com/mhuttner/miRA	http://dx.doi.org/10.1371/journal.pone.0057233
miRNA Digger	I	A, P	–	2016	–2016	http://www.benoslab.pitt.edu/Software/hhmmir_v1.2.zip	http://dx.doi.org/10.1038/srep18901
miRvial	I	A, P	–	2017	v0.0.4	https://github.com/SystemsBiologyOfJianghanUniversity/miRvial	http://dx.doi.org/10.1093/nar/gkx834
miRCat2	I	A, P	–	2017	v4.5	http://srna-workbench.cmp.uea.ac.uk/mircat2/	http://dx.doi.org/10.1093/bioinformatics/btx210
triplet–SVM	II	A, P	SVM	2005	–2005	http://bioinfo.au.tsinghua.edu.cn/mirnasvm/	http://dx.doi.org/10.1093/nar/gkm368
MiPred	II	A, P	RF	2007	v0.1	http://server.malab.cn/MiPred/	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-S1-S35
miRanalyzer	I & II	A, P	RF	2009	v0.3	http://bioinfo2.ugr.es/miRanalyzer/standalone.html	https://pubmed.ncbi.nlm.nih.gov/21515631/
HHMMiR	II	A, P	HHMM	2009	v1.2	http://biodev.hgen.pitt.edu/kadriAPBC2009.html	http://dx.doi.org/10.1093/nar/gkp347
miReader	I & II	A, P	BF-trees	2013	–2016	http://scbb.ihbt.res.in/2810-12/miReader.php	http://dx.doi.org/10.1371/journal.pone.0066857
miRPlex	I & II	A, P	SVM	2013	v0.1	https://sourceforge.net/projects/mirplex/	http://dx.doi.org/10.1002/jez.b.v320.1
miRLocator	II	P	RF	2015	–2017	https://github.com/cma2015/miRLocator	http://dx.doi.org/10.1371/journal.pone.0142753
plantMirP	II	P	SVM	2016	v1.0.0	https://github.com/yygen89/plantMirP	http://dx.doi.org/10.1039/C6MB00295A
deepSOM	II	A, P	SOMs	2017	v0.19	http://fich.unl.edu.ar/sinc/blog/web-demo/deepsom/	https://ieeexplore.ieee.org/abstract/document/7484734/
Mirnovo	I & II	A, P	RF	2017	v1.0	http://wwwdev.ebi.ac.uk/enright-dev/mirnovo/	https://academic.oup.com/nar/article/45/21/e177/4210935
miRHunter	II	A, P	SVM	2017	–	NA	https://link.springer.com/article/10.1007/s13206-017-1210-3
miRNA-dis	II	A, P	SVM	2017	–	http://bioinformatics.hitsz.edu.cn/miRNA-dis/	https://pubs.rsc.org/en/content/articlelanding/2015/MB/C5MB00050E#!divAbstract
microRPM	I & II	P	SVM	2017	–2018	http://microrpm.itps.ncku.edu.tw/	https://academic.oup.com/bib/article/20/5/1607/5001762

Note: Category: homology (H),signature (I), machine learning (II); Organism: animal (A), plant (P); ML(machine learning) method: support vector machine (SVM), random forest (RF),hierarchical hidden Markov model (HHMM), best-first trees (BF-trees),Self-organizing maps (SOMs).