Below the table of selected tools is shown. Each row corresponds to one tool while each column identifies a feature about methods collected from the literature. You can search through all data cells using the search bar in the top-right corner. Also, you can filter along each column using the input fields below the column header. Data can be exported to several common formats using the respective buttons at the top-left of the table. Individual columns can be hidden from the view using the "Column visibility" button. To sort along a single column click on the associated column header. To sort along several columns click on the column headers in order, each time holding the shift button pressed.

Please note that some columns are invisible by default. They can be accessed via the "Column visibility" button.

Index Tool Web server (Method)? Download (Method)? Download (Default predictions)? MicroRNA organism? Target organism? Machine learning based? Underlying method? Used target principle(s)? Requires NGS data for a user run? Input data type? Validation data type? Offers downstream analysis, e.g. pathway enrichments? Uses predictions from other published tool(s), i.e. non ab initio? Which other tools are preprocessed? Prediction granularity? Implemented in? Journal / Conference? Target region? Input format miRNAs? Input format targets? Other input format(s)? Output format? Main output type(s)? Novel miRNAs? Novel targets? Number of Features? (Machine learning only) Year of last update? (until February 2019) Year? Times cited?(04.02.2019) Publication doi url? Official link(s)? Utility tool? Full toolname
1 Antar No No Yes Homo sapiens, Mus musculus Homo sapiens, Mus musculus Yes Random Forest Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental No Yes miRanda Per whole target N/A RNA 3’ UTR N/A N/A N/A N/A Probability, Binary N/A N/A 20 N/A 2011 41 https://dx.doi.org/10.1261%2Frna.2387911 http://servers.binf.ku.dk/antar/ No Antar
2 Avishkar No Yes No Homo sapiens, Mus musculus Homo sapiens, Mus musculus Yes Support Vector Machine Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental No Yes RNAhybrid Per binding site Python BMC Genomics Any Comma separated table (Name, sequence) Comma separated table (Name, sequence) CLIP locations as comma separated table Custom table format Probability, Binary Yes Yes 13 2017 2015 9 https://dx.doi.org/10.1186%2Fs12864-015-1933-2, Erratum https://doi.org/10.1186/s12864-016-2367-1 https://bitbucket.org/cellsandmachines/avishkar No Avishkar
3 BcmicrO Yes No Yes Homo sapiens, Mus musculus Homo sapiens, Mus musculus Yes Bayesian Network Sequence compl., Structure, Site Accessibility No Both Experimental No Yes miRanda, TargetScan Per whole target N/A BMC Genomics 3’ UTR N/A N/A N/A N/A Probability N/A N/A N/A N/A 2012 5 https://doi.org/10.1186/1471-2164-13-S8-S13, https://www.ncbi.nlm.nih.gov/pubmed/23282032/ http://compgenomics.utsa.edu/gene/gene_1.php No BcmicrO
4 Bi-Targeting No Yes Yes Homo sapiens Homo sapiens No Dynamic programming Sequence compl., Structure No Both Experimental Yes No Both Java BMC Bioinformatics 3’ UTR Fasta Fasta Custom table format Duplex energy, hypergeometric p-value Yes Yes N/A N/A 2010 13 https://dx.doi.org/10.1186%2F1471-2105-11-249 http://www.cs.bgu.ac.il/~vaksler/BiTargeting.htm No Bi-Targeting
5 BioVLAB-MMIA Yes No No Homo sapiens, Mus musculus Homo sapiens, Mus musculus No Correlation analysis Sequence compl., Structure, Site Accessibility No Both Experimental Yes Yes TargetScan Per whole target Java Bioinformatics Any SIP (Array), Fastq (NGS) SIP (Array), Fastq (NGS) Custom table format P-value / fold change Yes No N/A N/A 2015 14 https://doi.org/10.1093/bioinformatics/btu614 http://epigenomics.snu.ac.kr/biovlab_mmia_ngs/ Yes BioVLAB-MMIA-NGS
6 Chan et al. No Yes Yes Caenorhabditis elegans, Drosophila melanogaster Caenorhabditis elegans, Drosophila melanogaster No Motif discovery, Statistical Analysis Conservation No Sequence Artificial Yes No Both N/A PLOS Computational Biology 3’ UTR N/A N/A N/A N/A Conservation scores N/A N/A N/A N/A 2005 62 https://doi.org/10.1371/journal.pcbi.0010069 http://tavazoielab.princeton.edu/mirnas/ No Chan et al.
7 ChemiRs Yes No No Homo sapiens Homo sapiens No Tool ensemble Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental Yes Yes miRanda, RNAhybrid, TargetScan, DIANA-microT Per whole target Java BMC Bioinformatics 3’ UTR Identifier list Identifier list Comma separated values file Binary decision No No N/A 2016 2016 4 https://doi.org/10.1186/s12859-016-1002-0 http://omics.biol.ntnu.edu.tw/ChemiRs No ChemiRs
8 chimiRic No Yes No Homo sapiens, Mus musculus, Caenorhabditis elegans Homo sapiens, Mus musculus, Caenorhabditis elegans Yes Support Vector Machine Sequence compl. No Sequence Experimental No No Per binding site Python PLOS Computational Biology 3’ UTR N/A N/A N/A N/A Score Yes Yes N/A 2016 2016 5 https://dx.doi.org/10.1371%2Fjournal.pcbi.1005026 https://bitbucket.org/leslielab/chimiric No chimiRic
9 CleaveLand4 No Yes No Any Any No Rule-based Sequence compl., Structure, Conservation Yes Both Experimental No No Per binding site Perl, R Bioinformatics Any Fasta Fasta Fasta for degradome-seq reads, Optional fasta to filter structural RNAs Custom list format Score Yes Yes N/A 2018 2009, 2014 229, 40 https://doi.org/10.1093/bioinformatics/btn604, https://doi.org/10.1093/nar/gku157 https://github.com/MikeAxtell/CleaveLand4/releases, http://sites.psu.edu/axtell/software/cleaveland4/ No CleaveLand4
10 CoMeTa No No Yes Homo sapiens Homo sapiens No Expression correlation Sequence compl., Structure, Conservation No Expression Experimental Yes Yes miRanda, TargetScan Per whole target N/A Genome Research 3’ UTR N/A N/A N/A Custom table format Rank percentile No No N/A N/A 2012 92 https://dx.doi.org/10.1101%2Fgr.130435.111 http://cometa.tigem.it/index.php No CoMeTa
11 ComiR Yes Yes Yes Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Yes Support Vector Machine Sequence compl., Structure, Site Accessibility No Both Experimental No Yes miRanda Per whole target R PLOS Computational Biology 3’ UTR Comma separated field format table (with expression), List of miRNA IDs (without expression) Fasta Tab separated values file Probability No Yes 4 2015 2012 20, 104 https://doi.org/10.1371/journal.pcbi.1002830, https://doi.org/10.1093/nar/gkt379 http://www.benoslab.pitt.edu/comir/ No ComiR
12 CPSS 2.0 Yes No No Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster, Acyrthosiphon pisum, Aegilops tauschii, Amborella trichopoda, Anolis carolinensis, Anopheles gambiae, Apis mellifera, Arabidopsis lyrata, Arabidopsis thaliana, Bombyx mori, Bos taurus, Brachypodium distachyon, Brassica rapa Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster, Acyrthosiphon pisum, Aegilops tauschii, Amborella trichopoda, Anolis carolinensis, Anopheles gambiae, Apis mellifera, Arabidopsis lyrata, Arabidopsis thaliana, Bombyx mori, Bos taurus, Brachypodium distachyon, Brassica rapa No Score Sequence compl., Structure Yes Both None Yes Yes miRanda Per whole target Perl, PHP Bioinformatics Any Fasta (raw sequencing reads) None Tab separated values file Score Yes No N/A 2017 2012 28, 0 https://doi.org/10.1093/bioinformatics/bts282, https://doi.org/10.1093/bioinformatics/btx066 http://mcg.ustc.edu.cn/db/cpss/index.html, http://114.214.166.79/cpss2.0/ Yes CPSS 2.0
13 CUDA-miRanda No Yes No Any Any No Dynamic programming Sequence compl., Structure No Sequence Experimental No No N/A Both C, C++, CUDA BMC Medical Genomics 3’ UTR Fasta Fasta Custom list format Score Yes Yes N/A 2013 2014 6 https://dx.doi.org/10.1186%2F1755-8794-7-S1-S9 https://sourceforge.net/projects/cudamiranda/ No CUDA-miRanda (GAMUT)
14 Cupid No Yes No Homo sapiens Homo sapiens Yes Support Vector Machine Sequence compl., Structure, Site Accessibility, Conservation No Both Experimental No Yes miRanda, TargetScan Both Matlab Genome Research 3’ UTR Custom tab separated values file Custom tab separated values file containing precomputed targets Tab separated values file Probability / Binary decision Yes Yes 6 + 3 2018 2015 30 https://doi.org/10.1101/gr.178194.114 http://cupidtool.sourceforge.net/ No Cupid
15 DeAnnIso Yes No No Homo sapiens, Mus musculus, Drosophila melanogaster Homo sapiens, Mus musculus, Drosophila melanogaster No Score Sequence compl., Structure No Sequence None Yes Yes miRanda, RNAhybrid Per whole target Perl, R, PHP Nucleic Acids Research Any Fasta (isomiRs), 
Fasta (raw sequencing reads) Custom table format Score Yes No N/A 2016 2016 11 https://doi.org/10.1093/nar/gkw427 https://mcg.ustc.edu.cn/bsc/deanniso/index.html Yes DeAnnIso
16 DeepMirTar No Yes No Homo sapiens Homo sapiens Yes Deep learning Sequence compl., Structure, Site Accessibility, Conservation No Sequence Both No No Per binding site Python Bioinformatics 3’ UTR N/A N/A N/A N/A Binary decision Yes Yes 750 2018 2018 1 https://doi.org/10.1093/bioinformatics/bty424 https://github.com/Bjoux2/DeepMirTar_SdA No DeepMirTar
17 deepTarget No Yes No Homo sapiens Homo sapiens Yes Deep learning Sequence compl. No Sequence Both No No Per whole target Python Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics Any N/A N/A N/A N/A Binary decision Yes Yes N/A 2016 2016 5 https://doi.org/10.1145/2975167.2975212 http://data.snu.ac.kr/pub/deepTarget/ No deepTarget
18 DIANA-microT-CDS Yes No Yes Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Yes Generalized Linear Models Sequence compl., Structure, Site Accessibility, Conservation No Sequence Both Yes Yes RNAhybrid Both Java, R BMC Bioinformatics, Bioinformatics, Nucleic Acids Research, Genes and Development 3’ UTR, CDS Identifier Identifier Comma separated values file Score No No 15 N/A 2011, 2012, 2009, 2004 533, 230, 353, 70, 18, 210, 327 https://doi.org/10.1101/gad.1184704, https://doi.org/10.1186/1471-2105-10-295, https://doi.org/10.1093/nar/gkp292, https://doi.org/10.1093/nar/gkr294, https://doi.org/10.3389/fgene.2011.00103, https://doi.org/10.1093/bioinformatics/bts043, https://doi.org/10.1093/nar/gkt393 http://www.microrna.gr/microT-CDS, http://www.microrna.gr/webServer No DIANA-microT-CDS 5.0
19 ElMMo3 No No Yes Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Yes Bayesian inference Sequence compl., Conservation No Both Both Yes No Per whole target N/A BMC Bioinformatics, Nucleic Acids Research 3’ UTR N/A N/A N/A Tab separated values file Probability No No N/A N/A 2009, 2007 204, 57 https://doi.org/10.1186/1471-2105-8-69, https://dx.doi.org/10.1093%2Fnar%2Fgkp412 http://www.mirz.unibas.ch/ElMMo3/index.php No ElMMo3 (MIRZ)
20 Expmicro No Yes No Homo sapiens Homo sapiens Yes Bayesian Gaussian Mixture Model Sequence compl., Structure, Site Accessibility, Conservation No Both Both No No SVMicrO Per whole target N/A BMC Genomics 3’ UTR N/A N/A N/A N/A Score N/A N/A 2 N/A 2010 6 https://doi.org/10.1186/1471-2164-11-S3-S12 http://compgenomics.utsa.edu/expmicro.html, http://expmicro.cbi.utsa.edu/ No Expmicro
21 Fujiwara & Yada No No No Homo sapiens Homo sapiens No Statistical Analysis, Sequence search N/A No Sequence Experimental No No Per whole target N/A BMC Genomics Any N/A N/A N/A N/A P-value N/A N/A N/A N/A 2013 9 https://doi.org/10.1186/1471-2164-14-S2-S3 No Fujiwara & Yada
22 GenMir++ No Yes Yes Homo sapiens Homo sapiens Yes Bayesian inference Sequence compl., Site Accessibility No Both Experimental Yes Yes TargetScan Per whole target Matlab Nature Methods 3’ UTR Expression matrix Expression matrix Sequence based prediction matrix Score / Probability matrix Probability, Score Yes Yes N/A 2012 2007 287 https://doi.org/10.1038/nmeth1130 http://www.psi.toronto.edu/genmir/ No GenMir++
23 GUUGle Yes Yes No Any Any No Write-Only-Top-Down algorithm Sequence compl. No Sequence None No No Per binding site C Bioinformatics Any Fasta Fasta Custom list format Match length Yes Yes N/A N/A 2006 27 https://doi.org/10.1093/bioinformatics/btk041 https://bibiserv.cebitec.uni-bielefeld.de/guugle Yes GUUGle
24 homoTarget No Yes Yes Homo sapiens Homo sapiens Yes Pattern Recognition Neural Network Sequence compl., Structure No Sequence Experimental No No Per binding site C-sharp Elsevier Genomics 3’ UTR Fasta Fasta Custom list format Binary decision Yes Yes 12 2012 2013 12 https://doi.org/10.1016/j.ygeno.2012.11.005 https://lbb.ut.ac.ir/dynamic/index.php?newsid=13 No homoTarget
25 HuMiTar No No No Homo sapiens Homo sapiens No Alignment, Scoring function Sequence compl. No Sequence Both No No Per binding site N/A Algorithms for Molecular Biology 3’ UTR N/A N/A N/A Score Yes Yes N/A 2008 2008 17 https://doi.org/10.1186/1748-7188-3-16 No HuMiTar
26 iMir No Yes No Any Any No Tool ensemble Sequence compl., Structure, Site Accessibility Yes Both None No Yes miRanda, TargetScan Per binding site Python, Java, Perl, R BMC Bioinformatics 3’ UTR Fastq Fastq Graphics / Text files Various Yes No N/A 2015 2013 34 https://doi.org/10.1186/1471-2105-14-362 http://www.labmedmolge.unisa.it/italiano/home/imir Yes iMir
27 IMTRBM No Yes No Homo sapiens Homo sapiens Yes Restricted Boltzmann machine Sequence compl., Structure, Site Accessibility No Sequence Experimental No Yes miRanda, TargetScan Per whole target Java IEEE Journal of Biomedical and Health Informatics Any Identifier list Identifier list Weighted and paired identifier list in tab-delimited file Tab separated values file Score Yes Yes N/A 2017 2018 0 https://doi.org/10.1109/JBHI.2018.2814609 https://github.com/liuying201705/IMTRBM No IMTRBM
28 IntaRNA 2.0 Yes Yes Yes Any Any No Hybridization, Matrix algorithms Sequence compl., Structure, Site Accessibility No Sequence Experimental No No Per whole target Perl, C++ Bioinformatics, Nucleic Acids Research Any Fasta Fasta CSV MFE Yes Yes N/A 2018 2008 27, 234 https://doi.org/10.1093/bioinformatics/btn544, https://doi.org/10.1093/nar/gkx279 https://github.com/BackofenLab/IntaRNA, http://rna.informatik.uni-freiburg.de/IntaRNA/Input.jsp No IntaRNA 2.0
29 MAGI Yes No No Homo sapiens Homo sapiens No Dynamic programming Sequence compl., Structure Yes Both None Yes Yes miRanda Both Perl, R, PHP, C, CUDA, Node.js, JavaScript Bioinformatics 3’ UTR, CDS Fastq Fastq Graphics / Custom table values Score Yes No N/A N/A 2014 13 https://doi.org/10.1093/bioinformatics/btu377 http://magi.ucsd.edu/ Yes MAGI
30 MAGIA2 Yes No No Homo sapiens, Mus musculus, Drosophila melanogaster Homo sapiens, Mus musculus, Drosophila melanogaster No Tool ensemble Sequence compl., Structure, Site Accessibility, Conservation No Both Experimental Yes Yes TargetScan, DIANA-microT, miRanda (mirSVR) Per whole target N/A Nucleic Acids Research Any Tab-delimited matrix Tab-delimited matrix Graphics / Custom table values Various No No N/A 2011 2012, 2010 62, 105 https://doi.org/10.1093/nar/gkq423, https://doi.org/10.1093/nar/gks460 http://gencomp.bio.unipd.it/magia, http://gencomp.bio.unipd.it/magia2 No MAGIA2
31 MBStar Yes Yes Yes Homo sapiens Homo sapiens Yes Random Forest Sequence compl., Structure, Site Accessibility No Sequence Both No No Both C Nature Scientific Reports 3’ UTR Fasta Fasta Tab-delimited file with two identifier columns Custom list format Score Yes Yes 31 structural + 340 sequence features but in total 40 are subselected to remain 2014 2015 14 https://doi.org/10.1038/srep08004 https://www.isical.ac.in/~bioinfo_miu/MBStar30.htm No MBStar
32 microCLIP No Yes No Homo sapiens Homo sapiens Yes Random Forest, Deep learning Sequence compl., Structure, Conservation Yes Both Experimental No No Per binding site Java, R Nature Communications 3’ UTR, CDS Fasta SAM / BAM Phastcons files, Gene annotation bed file Bed format Score Yes No 131 2018 2018 0 https://doi.org/10.1038/s41467-018-06046-y http://carolina.imis.athena-innovation.gr/diana_team/microCLIP/index.html No microCLIP
33 MicroInspector Yes No No Any Any No Alignment Sequence compl., Structure No Sequence None No No Per binding site Perl Nucleic Acids Research 3’ UTR Pre-defined selection Sequence CSV MFE No Yes N/A N/A 2005 172 https://doi.org/10.1093/nar/gki364 http://www.imbb.forth.gr/microinspector No MicroInspector
34 microMUMMIE No Yes No Homo sapiens Homo sapiens No Hidden Markov Model Sequence compl., Conservation Yes Sequence Both No No Per binding site Perl, C Nature Methods 3’ UTR Custom Custom Read cluster files (CSV), Genomic annotation files (Tab-delimited) CSV Signal to noise ratio Yes Yes N/A 2015 2013 31 https://doi.org/10.1038/nmeth.2489 https://ohlerlab.mdc-berlin.de/software/microMUMMIE_99/ No microMUMMIE
35 MicroTar No Yes No Metazoa Metazoa No Statistical Analysis, Rule-based Sequence compl., Structure, Site Accessibility No Sequence Both No No Per whole target C BMC Bioinformatics Any Fasta Fasta Tab separated values file MFE Yes Yes N/A 2008 2006 66 https://doi.org/10.1186/1471-2105-7-S5-S20 http://tiger.dbs.nus.edu.sg/microtar/ No MicroTar
36 mimiRNA Yes No No Homo sapiens Homo sapiens No Expression correlation Sequence compl., Structure, Site Accessibility No Expression Experimental No Yes TargetScan Per whole target N/A Bioinformatics Any N/A N/A N/A Custom list format None No No N/A 2009 2009 53 https://doi.org/10.1093/bioinformatics/btp649 http://mimirna.centenary.org.au/ Yes mimiRNA
37 MinoTar No No Yes Homo sapiens, Drosophila melanogaster Homo sapiens, Drosophila melanogaster No Probabilistic modelling Sequence compl., Conservation No Sequence Experimental No No Per whole target N/A PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Any N/A N/A N/A Comma separated values file Probability No No N/A 2010 2010 86 https://doi.org/10.1073/pnas.1006172107 http://www.minotar.csail.mit.edu/ No MinoTar
38 MirAncesTar No Yes Yes Homo sapiens Homo sapiens Yes Logistic regression Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental No Yes miRanda, RNAhybrid, TargetScan Per whole target Java Nucleic Acids Research 3’ UTR, 5’ UTR None Custom tab separated values file Phastcons files, Custom tab separated values file Custom list format Score Yes No N/A 2016 2016 5 https://doi.org/10.1093/nar/gkw1085 https://www.cs.mcgill.ca/~blanchem/mirancestar/ No MirAncesTar
39 miRanda No Yes No Any Any No Dynamic programming Sequence compl., Structure No Sequence Both No No Both C Genome Biology, PLOS Biology 3’ UTR Fasta Fasta Custom list format Score, MFE Yes Yes N/A 2010 2003 608 https://doi.org/10.1186/gb-2003-5-1-r1, Correction: https://doi.org/10.1371/journal.pbio.0030264 http://www.microrna.org/microrna/home.do No miRanda
40 miRaw No Yes No Homo sapiens Homo sapiens Yes Deep learning Sequence compl., Structure, Site Accessibility No Sequence Experimental No No Both Java PLOS Computational Biology 3’ UTR Binary decision Yes Yes N/A 2018 2018 0 https://doi.org/10.1371/journal.pcbi.1006185 https://bitbucket.org/account/user/bipous/projects/MIRAW No miRaw
41 miRcode Yes No Yes Homo sapiens Homo sapiens No Simple string match Sequence compl., Conservation No Sequence None No No Per binding site Perl, PHP, Matlab Bioinformatics Any Identifier Identifier Custom table format Conservation scores No No N/A 2012 2012 158 https://doi.org/10.1093/bioinformatics/bts344 http://www.mircode.org No miRcode
42 mirConnX Yes No No Homo sapiens, Mus musculus Homo sapiens, Mus musculus No Tool ensemble Sequence compl., Structure, Conservation No Both Experimental Yes Yes miRanda, RNAhybrid, TargetScan, PITA Per whole target N/A Nucleic Acids Research 3’ UTR Tab-delimited expression matrix Tab-delimited expression matrix Tab separated values file Score No No N/A 2011 2011 72 https://doi.org/10.1093/nar/gkr276 http://www.benoslab.pitt.edu/mirconnx No mirConnX
43 mirCoX Yes No Yes Homo sapiens Homo sapiens No Expression correlation Expression level Yes Expression Experimental No No N/A Per whole target Python, R, C++ BMC Bioinformatics Any N/A N/A N/A Comma separated values file Correlation No No N/A 2012 2013 13 https://doi.org/10.1186/1471-2105-14-S14-S17 http://210.212.254.116/mircox/pages/index.php Yes mirCoX
44 miREE Yes No No Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Yes Support Vector Machine, Genetic algorithm Sequence compl., Structure, Site Accessibility No Sequence Both No No Per binding site N/A BMC Bioinformatics 3’ UTR Fasta Fasta N/A Score No No 25 N/A 2011 20 https://doi.org/10.1186/1471-2105-12-454 http://eda.polito.it/miREE/ No miREE
45 miRepress Yes Yes No Homo sapiens Homo sapiens Yes Artificial Neural Network Sequence compl., Conservation No Sequence Artificial No No Per whole target Java Nature Scientific Reports Any N/A N/A N/A Fold-repression N/A N/A 9 N/A 2016 0 https://doi.org/10.1038/srep22334 http://gyanxet-beta.com/mirepress.jsp No miRepress
46 MirMAP Yes Yes Yes Homo sapiens, Mus musculus, Bos taurus Homo sapiens, Mus musculus, Bos taurus No Motif discovery, Markov Model Structure, Site Accessibility, Conservation No Sequence Experimental No No Both Python Nucleic Acids Research 3’ UTR List of identifier and sequence List of identifier and sequence Multi species alignment of target sequences Custom report format Probability, Score, MFE Yes Yes 11 2013 2012, 2013 92 https://doi.org/10.1093/nar/gks901, https://doi.org/10.1093/nar/gkt430
 https://mirmap.ezlab.org No MirMAP
47 mirMark No Yes No Homo sapiens Homo sapiens Yes Random Forest Sequence compl., Structure, Site Accessibility, Conservation No Sequence Both No Yes miRanda Both Perl, R Genome Biology 3’ UTR Fasta Fasta Paired list of identifiers as tab separated values, 
Phastcons scores for targets N/A Probability Yes Yes >700 2014 2014 11 https://dx.doi.org/10.1186%2Fs13059-014-0500-5 https://github.com/lanagarmire/MirMark, https://mn.eng.hawaii.edu/~garmire/HTML/MirMark/ No mirMark
48 miRNALasso No Yes No Homo sapiens Homo sapiens Yes Lasso regression Sequence compl., Structure, Site Accessibility, Expression level No Both Experimental No Yes TargetScan Per whole target Matlab Bioinformatics 3’ UTR Expression matrix Expression matrix Sequence based prediction matrix Vector of Coefficients Score Yes Yes N/A 2015 2015 6 https://doi.org/10.1093/bioinformatics/btv392 http://nba.uth.tmc.edu/homepage/liu/miRNALasso No miRNALasso
49 miRror-Suite Yes No No Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster No Tool ensemble Sequence compl., Structure, Site Accessibility, Conservation, Expression level No Both Experimental Yes Yes TargetScan, miRanda (mirSVR), PITA Per whole target N/A Database Any Identifier list Identifier list Custom table format Probability, Score No No N/A 2010 2014 4 https://doi.org/10.1093/database/bau043 http://www.mirrorsuite.cs.huji.ac.il/ Yes miRror-Suite
50 mirSOM Yes Yes No Caenorhabditis elegans Caenorhabditis elegans Yes Self-organizing map Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental No No Both Java Bioinformatics 3’ UTR Fasta N/A Matrix Neuron weights Yes Yes N/A N/A 2011 8 https://doi.org/10.1093/bioinformatics/btr144 http://kokki.uku.fi/bioinformatics/mirsom, https://bioinformatics.uef.fi/mirsom/ No mirSOM
51 mirSVR No No Yes Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Yes Support Vector Machine Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental No Yes miRanda Per binding site C Genome Biology 3’ UTR N/A N/A N/A Tab separated values file Score No No 52 2010 2010 738 https://doi.org/10.1186/gb-2010-11-8-r90 http://www.microrna.org/microrna/home.do No mirSVR (microrna.org)
52 miRTar Yes No Yes Homo sapiens Homo sapiens No Tool ensemble Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental Yes Yes miRanda, RNAhybrid, TargetScan, PITA Both N/A BMC Bioinformatics Any Fasta, Identifier Identifier Custom table format, Custom list format, Graphics Score Yes No N/A N/A 2011 57 https://doi.org/10.1186/1471-2105-12-300 http://mirtar.mbc.nctu.edu.tw/ No miRTar
53 miRTar2GO Yes No Yes Homo sapiens Homo sapiens No Rule-based Sequence compl., Structure, Conservation No Sequence Experimental Yes No Per binding site N/A Nucleic Acids Research 3’ UTR Identifier Identifier CSV MFE No No N/A 2016 2016 2 https://doi.org/10.1093/nar/gkw1185 http://www.mirtar2go.org/ No miRTar2GO
54 miRTarCLIP No Yes No Homo sapiens, Mus musculus Homo sapiens, Mus musculus No Target site mining Sequence compl., Site Accessibility, Expression level Yes Both Experimental No Yes TargetScan Per binding site PHP BMC Genomics 3’ UTR Fastq Fastq TargetScan default predictions, 
3’ UTR sequences from TargetScan Tab separated values file Score No No N/A 2013 2013 27 https://doi.org/10.1186/1471-2164-14-S1-S2, https://www.ncbi.nlm.nih.gov/pubmed/23368412 http://mirtarclip.mbc.nctu.edu.tw/index.php No miRTarCLIP
55 MirTarget Yes No Yes Homo sapiens, Mus musculus Homo sapiens, Mus musculus Yes Support Vector Machine Sequence compl., Structure, Conservation No Sequence Experimental No No Per whole target Perl, R Bioinformatics, Nucleic Acids Research, Genome Biology Any Sequence Sequence Custom table format Score Yes Yes 96 2019 2016, 2014, 2007, 2006 0, 165, 382, 392, 55 https://doi.org/10.1093/nar/gkl068, https://doi.org/10.1093/bioinformatics/btm595, https://doi.org/10.1093/nar/gku1104, https://doi.org/10.1093/bioinformatics/btw002, https://doi.org/10.1186/s13059-019-1629-z
 http://mirdb.org No MirTarget V1-V6 (miRDB)
56 mirTarPri Yes No No Homo sapiens Homo sapiens No Information content theory Sequence compl., Structure, Site Accessibility No None Experimental Yes Yes miRanda, RNAhybrid, TargetScan, DIANA-microT, PITA Per whole target N/A PLoS One Any Identifier Identifier Custom table format Rank scores No No N/A 2013 2013 8 https://dx.doi.org/10.1371%2Fjournal.pone.0053685 http://www.bio-bigdata.com/mirTarPri/ No mirTarPri
57 miRTarVis+ Yes No No Homo sapiens, Mus musculus, Bos taurus Homo sapiens, Mus musculus, Bos taurus No Tool ensemble Sequence compl., Structure, Site Accessibility, Conservation, Expression level No Both Experimental Yes Yes TargetScan, miRanda (mirSVR) Per whole target Java BMC Proceedings Any Expression matrix Expression matrix Custom table format P-value, Fold change No No N/A 2017 2015 1, N/A https://dx.doi.org/10.1186%2F1753-6561-9-S6-S2, https://doi.org/10.1016/j.ymeth.2017.06.004 http://hcil.snu.ac.kr/~rati/miRTarVis/index.html, http://hcil.snu.ac.kr/research/mirtarvisplus Yes miRTarVis+
58 MiRTDL Yes Yes No Homo sapiens, Mus musculus Homo sapiens, Mus musculus Yes Deep learning Sequence compl., Structure, Site Accessibility, Conservation No Sequence Both No No Per binding site Matlab IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS Any Matrix of pairs versus feature values N/A Binary decision Yes Yes 20 2016 2016 7 https://doi.org/10.1109/TCBB.2015.2510002 http://nclab.hit.edu.cn/ccrm No MiRTDL
59 MiRTif Yes No No Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Yes Support Vector Machine Sequence compl., Structure No Sequence Both No Yes RNAhybrid Per binding site N/A BMC Bioinformatics Any Fasta containing miRNA-target site duplexes Custom list format Probability, Binary decision Yes Yes 465 2008 2008 42 https://doi.org/10.1186/1471-2105-9-S12-S4 http://bsal.ym.edu.tw/mirtif No MiRTif
60 mirTools 2.0 Yes Yes No Metazoa Metazoa No Tool ensemble Sequence compl., Structure, Site Accessibility Yes Sequence None Yes Yes miRanda, RNAhybrid, TargetScan Both Perl, R RNA Biology Any Fasta / Sam Fasta / Sam Custom table format Score Yes No N/A 2013 2010, 2013 40, 81 https://doi.org/10.1093/nar/gkq393, https://doi.org/10.4161/rna.25193 http://www.wzgenomics.cn/mr2_dev/ Yes mirTools 2.0
61 mirWIP Yes Yes Yes Caenorhabditis elegans Caenorhabditis elegans No Statistical Analysis, Rule-based Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental No Yes RNAhybrid Both Python Nature Methods 3’ UTR N/A N/A N/A N/A Score Yes Yes N/A N/A 2008 139 https://doi.org/10.1038/nmeth.1247 http://mirtargets.org/, http://sfold.wadsworth.org/cgi-bin/index.pl No mirWIP
62 MIRZA No Yes No Homo sapiens Homo sapiens No Biophysical model Sequence compl., Structure No Both Both No No Per binding site C++ Nature Methods 3’ UTR Fasta Fasta Custom table format Score Yes Yes N/A 2018 2013 78 https://doi.org/10.1038/nmeth.2341 http://www.clipz.unibas.ch/, https://github.com/zavolanlab/Dockerfiles, http://www.clipz.unibas.ch/mirzag/ No MIRZA
63 MIRZA-G No Yes Yes Homo sapiens Homo sapiens No Biophysical model Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental No Yes MIRZA Both Python, C++ Nucleic Acids Research 3’ UTR Fasta Fasta Custom table format Probability Yes Yes N/A 2018 2015 19 https://doi.org/10.1093/nar/gkv050, Correction: https://doi.org/10.1093/nar/gkv924 http://www.clipz.unibas.ch/mirzag/ No MIRZA-G
64 miSTAR Yes No No Homo sapiens Homo sapiens Yes Random Forest, Logistic regression Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental No No Per whole target R Nucleic Acids Research 3’ UTR Identifier Identifier Custom list format Probability No No 53 2016 2016 4 https://doi.org/10.1093/nar/gkw1260 http://www.mi-star.org/ No miSTAR
65 miTarget Yes No N/A Homo sapiens Homo sapiens Yes Support Vector Machine Sequence compl., Structure No Sequence Experimental No No Per binding site Python, C BMC Bioinformatics 3’ UTR N/A N/A N/A N/A Score N/A N/A 41 2006 2006 4 https://dx.doi.org/10.1186%2F1471-2105-7-411 http://cbit.snu.ac.kr/~miTarget No miTarget
66 MMIA Yes No N/A Homo sapiens Homo sapiens No Tool ensemble, Expression correlation Sequence compl., Structure, Site Accessibility, Conservation, Expression level No Both Experimental Yes Yes TargetScan, PITA Per whole target N/A Nucleic Acids Research 3’ UTR Tab-delimited expression file Tab-delimited expression file Graphics / Custom table values Fold change No No N/A N/A 2009 110 https://doi.org/10.1093/nar/gkp294 http://cancer.informatics.indiana.edu/mmia Yes MMIA
67 MovingTargets No No No Drosophila melanogaster Drosophila melanogaster No Rule-based Sequence compl., Structure, Conservation No Sequence Experimental No No Per binding site Perl BMC Genomics 3’ UTR N/A N/A N/A N/A MFE N/A N/A N/A 2005 2005 53 https://dx.doi.org/10.1186%2F1471-2164-6-88 No MovingTargets
68 MTar No No No Homo sapiens Homo sapiens Yes Artificial Neural Network Sequence compl., Structure No Sequence Experimental No No Per binding site N/A BMC Bioinformatics Any N/A N/A N/A Custom list format MFE, Binding class N/A N/A 16 2010 34 https://doi.org/10.1186/1471-2105-11-S1-S2 No MTar
69 MultiMiTar Yes Yes Yes Homo sapiens Homo sapiens Yes Support Vector Machine Sequence compl., Site Accessibility No Sequence Experimental No No Per whole target C, C++ PLoS One 3’ UTR Fasta Fasta Tab-delimited file with two identifier columns HTML table Rank scores Yes Yes 90 N/A 2011 25 https://doi.org/10.1371/journal.pone.0024583 http://www.isical.ac.in/~bioinfo_miu/multimitar.htm No MultiMiTar
70 myMIR Yes No No Homo sapiens, Mus musculus Homo sapiens, Mus musculus No Tool ensemble Sequence compl., Structure, Site Accessibility, Conservation, Expression level No Both Experimental Yes Yes miRanda, RNAhybrid, TargetScan, DIANA-microT, PITA Per binding site Perl Briefings in Bioinformatics 3’ UTR Identifier list, Sequence Identifier list Custom table format Scores Yes No N/A N/A 2011 18 https://doi.org/10.1093/bib/bbr062 http://www.itb.cnr.it/micro/ No myMIR
71 NbmiRTar No Yes No Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Yes Naive Bayes Sequence compl., Structure No Sequence Both No Yes miRanda Per whole target N/A Bioinformatics 3’ UTR Sequence Sequence N/A Scores Yes Yes 57 2007 2007 79 https://doi.org/10.1093/bioinformatics/btm484 http://wotan.wistar.upenn.edu/NBmiRTar/ No NbmiRTar
72 Nucleus No No No Drosophila melanogaster Drosophila melanogaster No Hybridization Structure No Sequence Both No No Per binding site N/A Developmental Biology 3’ UTR N/A N/A N/A N/A Score, MFE Yes Yes N/A 2004 2004 213 https://doi.org/10.1016/j.ydbio.2003.12.003 No Nucleus
73 Oasis 2.0 Yes No No Metazoa Metazoa Yes Random Forest Expression level No Expression None Yes No Per whole target Python, Java, R, PHP, JavaScript BMC Bioinformatics, Bioinformatics Any Fastq Custom table format Feature importance, Predicted targets Yes No N/A 2016 2015, 2018 2, 24 https://doi.org/10.1093/bioinformatics/btv113, https://doi.org/10.1186/s12859-018-2047-z http://oasis.dzne.de/ Yes Oasis 2.0
74 PACCMIT-CDS No Yes Yes Homo sapiens Homo sapiens No Statistical Analysis Sequence compl., Site Accessibility, Conservation No Sequence Both No No Per whole target C, C++ RNA, Nucleic Acids Research, PLoS One 3’ UTR Fasta Fasta with multiway alignments Custom list format Probability Yes Yes N/A 2013 2015, 2012, 2010, 2013 4, 17, 54, 15 https://doi.org/10.1093/nar/gkq768, https://dx.doi.org/10.1371%2Fjournal.pone.0032208, https://doi.org/10.1261/rna.035634.112, https://doi.org/10.1093/nar/gkv457 http://paccmit.epfl.ch/, https://lcpt.epfl.ch/research/biophysics_and_bioinformatics/microrna_target_predictions/ No PACMIT, 
PACCMIT, 
PACCMIT-CDS
75 PicTar Yes No Yes Caenorhabditis elegans, Drosophila melanogaster, Vertebrata Caenorhabditis elegans, Drosophila melanogaster, Vertebrata No Statistical Analysis Sequence compl., Structure, Conservation No Sequence Both No No Both N/A Nature Genetics 3’ UTR N/A N/A Probability, Score Yes N/A N/A 2007 2005 3161 https://doi.org/10.1038/ng1536 https://pictar.mdc-berlin.de No PicTar
76 PITA Yes Yes Yes Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster No Thermodynamic model Sequence compl., Site Accessibility No Sequence Both No No Both Perl, C Nature Genetics 3’ UTR Fasta Fasta Custom list format Score Yes Yes N/A 2008 2007 1361 https://doi.org/10.1038/ng2135 http://genie.weizmann.ac.il/pubs/mir07 No PITA
77 RepTar Yes No N/A Homo sapiens, Mus musculus Homo sapiens, Mus musculus No Motif discovery, Hidden Markov Model Structure No Sequence Experimental No No Per binding site N/A Nucleic Acids Research 3’ UTR Identifier Identifier Custom list format Score, MFE No No N/A N/A 2010 28 https://doi.org/10.1093/nar/gkq1233 http://reptar.ekmd.huji.ac.il/ No RepTar
78 RNA22 Yes No Yes Metazoa Metazoa No Statistical Analysis, Pattern recognition Structure No Sequence Both No No Per binding site N/A Cell 3’ UTR Fasta Fasta Custom list format P-value, MFE Yes Yes N/A 2015 2006 1099 https://doi.org/10.1016/j.cell.2006.07.031 https://cm.jefferson.edu/rna22/ No RNA22
79 RNAhybrid Yes Yes No Any Any No Dynamic programming, Statistical Analysis Structure No Sequence Both No No Per binding site C Nucleic Acids Research 3’ UTR Fasta Fasta Custom list format P-value, MFE Yes Yes N/A N/A 2004, 2006 1261, 581 https://doi.org/10.1261/rna.5248604, https://doi.org/10.1093/nar/gkl243 http://bibiserv.techfak.uni-bielefeld.de/rnahybrid No RNAhybrid
80 Robins et al. No No No Drosophila melanogaster Drosophila melanogaster No Rule-based Sequence compl., Structure No Sequence Experimental No No Both N/A PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 3’ UTR N/A N/A N/A P-value N/A N/A N/A N/A 2005 163 https://doi.org/10.1073/pnas.0500775102 No Robins et al.
81 SeedVicious Yes Yes No Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster No Rule-based Sequence compl., Structure, Conservation No Sequence Experimental No No Per binding site Perl PLoS One 3’ UTR Fasta Fasta NEWICK tree file Custom list format MFE Yes Yes N/A 2018 2018 0 https://doi.org/10.1371/journal.pone.0195532 https://seedvicious.essex.ac.uk No SeedVicious
82 sRNAtoolbox Yes No No Any Any No Tool ensemble, Simple string match Sequence compl., Structure, Site Accessibility No Sequence Experimental Yes Yes miRanda, PITA Per binding site Java Nucleic Acids Research 3’ UTR Fasta Fasta Custom list format Score by number of programs Yes Yes N/A 2018 2015 69 https://doi.org/10.1093/nar/gkv555 http://bioinfo5.ugr.es/srnatoolbox Yes sRNAtoolbox
83 Stark et al. I No No Yes Drosophila melanogaster Drosophila melanogaster No Statistical Analysis, Hidden Markov Model Sequence compl., Structure, Conservation No Sequence Both No No Per binding site N/A PLOS Biology 3’ UTR N/A N/A N/A N/A Z score N/A N/A N/A N/A 2003 500 https://dx.doi.org/10.1371%2Fjournal.pbio.0000060 http://www.mirna.embl.de/ No Stark et al. I (EMBL)
84 Stark et al. II No No Yes Drosophila melanogaster Drosophila melanogaster No Statistical Analysis, Rule-based Sequence compl., Structure, Conservation No Sequence Both Yes Yes RNAhybrid Per binding site N/A Cell 3’ UTR N/A N/A N/A N/A P-value N/A N/A N/A N/A 2005 761 https://doi.org/10.1016/j.cell.2005.11.023 http://www.mirna.embl.de/ No Stark et al. II (EMBL)
85 STarMir Yes No No Homo sapiens, Mus musculus, Caenorhabditis elegans Any Yes Logistic regression Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental No Yes RNAhybrid Per binding site N/A Nucleic Acids Research Any Fasta, Identifier Fasta, Sequence Custom list format Binary decision Yes Yes 22 N/A 2014, 2013 41 https://doi.org/10.1093/nar/gkt435, https://doi.org/10.1093/nar/gku376 http://sfold.wadsworth.org/cgi-bin/starmirtest2.pl No STarMir
86 SuperMirTar No No No Homo sapiens Homo sapiens Yes Kernel-Based Supervised Distance Metric Learning, Embedding Sequence compl., Structure No Sequence Artificial No Yes RNAhybrid Per binding site Java IEEE Journal of Biomedical and Health Informatics 3’ UTR N/A N/A N/A Probability, Score N/A N/A 14 N/A 2013 1 https://doi.org/10.1109/TITB.2012.2229286 No SuperMirTar
87 SVMicrO No Yes Yes Homo sapiens, Mus musculus Homo sapiens, Mus musculus Yes Support Vector Machine Sequence compl., Structure, Site Accessibility, Conservation No Sequence Experimental No No Both C BMC Bioinformatics 3’ UTR N/A N/A N/A N/A Probability, Binary, Score N/A N/A 21 + 18 N/A 2010 43 https://doi.org/10.1186/1471-2105-11-476 http://compgenomics.utsa.edu/svmicro.html No SVMicrO
88 TaLasso Yes Yes No Homo sapiens Homo sapiens Yes Lasso regression Sequence compl., Structure, Expression level No Both Experimental Yes Yes miRanda Per whole target R, Matlab PLoS One Any N/A N/A N/A N/A Score No No N/A N/A 2012 35 https://doi.org/10.1371/journal.pone.0030766 http://talasso.cnb.csic.es/ No TaLasso
89 TargetBoost Yes No No Caenorhabditis elegans, Drosophila melanogaster Caenorhabditis elegans, Drosophila melanogaster Yes Genetic algorithm Sequence compl. No Sequence Both No No Per binding site N/A RNA 3’ UTR N/A N/A N/A N/A Probability N/A N/A N/A N/A 2005 81 https://dx.doi.org/10.1261%2Frna.7290705 http://www.interagon.com/demo/ No TargetBoost
90 TargetExpress Yes Yes Yes Homo sapiens, Mus musculus Homo sapiens, Mus musculus Yes Support Vector Machine Sequence compl., Structure, Conservation, Expression level No Both Experimental No Yes TargetScan, MIRZA Both Perl BMC Genomics 3’ UTR Expression table (Tab-separated values) Expression table (Tab-separated values) Custom list format Score No No N/A 2016 2016 7 https://doi.org/10.1186/s12864-016-2695-1 http://targetexpress.ceiabreulab.org/ No TargetExpress
91 TargetMiner Yes Yes Yes Homo sapiens Homo sapiens Yes Support Vector Machine Sequence compl., Site Accessibility, Conservation No Both Both No Yes miRanda, TargetScan, DIANA-microT Per whole target N/A Bioinformatics 3’ UTR Fasta Fasta Custom list format Score Yes Yes 90 2012 2009 123 https://doi.org/10.1093/bioinformatics/btp503 https://www.isical.ac.in/~bioinfo_miu/targetminer20.htm No TargetMiner
92 TargetRank Yes No Yes Homo sapiens, Mus musculus Homo sapiens, Mus musculus No Score Sequence compl., Conservation No Sequence Experimental No No Both R RNA 3’ UTR Identifier, Sequence Custom list format Rank score Yes No 4 N/A 2007 226 https://doi.org/10.1261/rna.768207 http://genes.mit.edu/targetrank/ No TargetRank
93 TargetScan Yes Yes Yes Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster Yes Rule-based, Stepwise regression Sequence compl., Site Accessibility, Conservation No Sequence Both No No Per binding site Perl Genome Research, Cell 3’ UTR Tab-delimited file Custom Phylogenetic tree file Tab separated values file Context++ score, PCT score Yes Yes 15 2018 2011, 2015, 2005, 2014, 2018, 2007, 2008, 2003 1, 3320, 7534, 2359, 4016, 481, 102, 1051 https://doi.org/10.1016/S0092-8674(03)01018-3, https://doi.org/10.1016/j.cell.2004.12.035, https://doi.org/10.1016/j.molcel.2007.06.017, https://doi.org/10.1101/gr.082701.108, https://dx.doi.org/10.1038%2Fnsmb.2115, https://dx.doi.org/10.1016%2Fj.molcel.2014.02.013, https://dx.doi.org/10.7554%2FeLife.05005, 
https://doi.org/10.1186/s13059-018-1504-3 www.targetscan.org No TargetScan
94 targetScore No Yes No Homo sapiens Homo sapiens Yes Variational Bayesian–Gaussian Mixture Model Sequence compl., Site Accessibility, Conservation, Expression level No Both Experimental Yes Yes TargetScan Per whole target R Bioinformatics Any Vector of fold-changes Matrix of sequence-scores Vector of scores Probability, Score Yes Yes N/A 2018 2013 16 https://doi.org/10.1093/bioinformatics/btt599 http://www.bioconductor.org/packages/release/bioc/html/TargetScore.html No targetScore
95 TargetSpy Yes Yes Yes Homo sapiens, Mus musculus, Drosophila melanogaster Homo sapiens, Mus musculus, Drosophila melanogaster Yes Free energy screening, Boosting Sequence compl., Structure, Site Accessibility No Sequence Experimental No No Per binding site Java BMC Bioinformatics 3’ UTR Fasta Fasta Custom list format (tab separated values) Probability, Score, MFE Yes Yes 45 2009 2010 88 https://doi.org/10.1186/1471-2105-11-292 http://webclu.bio.wzw.tum.de/targetspy/index.php?down=true No TargetSpy
96 TargetThermo No Yes No Homo sapiens, Drosophila melanogaster Homo sapiens, Drosophila melanogaster Yes Linear regression Sequence compl., Structure, Site Accessibility No Sequence Both No No Per whole target Perl PLoS One 3’ UTR Fasta Fasta Tab separated values file Predicted fold-change Yes Yes N/A 2011 2011 15 https://doi.org/10.1371/journal.pone.0020622 https://ohlerlab.mdc-berlin.de/software/TargetThermo_83/ No TargetThermo
97 TarPmiR No Yes No Homo sapiens, Mus musculus Homo sapiens, Mus musculus Yes Random Forest Sequence compl., Structure, Site Accessibility, Conservation No Sequence Both No No Per binding site Python Bioinformatics Any Fasta Fasta Custom list format (tab separated values) Probability Yes Yes 18(13) 2016 2016 8 https://doi.org/10.1093/bioinformatics/btw318 http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/ No TarPmiR
98 wapRNA Yes Yes No Any Any No Tool ensemble Sequence compl., Structure Yes Sequence Experimental Yes Yes miRanda, RNAhybrid Both Java Bioinformatics 3’ UTR Csfasta / fastq N/A N/A Score, MFE Yes Yes N/A 2011 2011 35 https://doi.org/10.1093/bioinformatics/btr504 http://waprna.big.ac.cn/ Yes wapRNA
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