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miRNA annotation tools for plants and animals

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Post time 2021-6-9 12:26:02 | Show all posts |Read mode
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).

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