Table 3.
Selected other functional miRNA tools
| Tool name | Brief introduction | Organism | Publication span | Last update | Current version | Platform | Link | References |
|---|---|---|---|---|---|---|---|---|
| ViennaRNA | RNA secondary structure predictor | A, P | 2003–15 | 2018 | v2.4.7 | WB, SA | http://rna.tbi.univie.ac.at/ | [51] |
| miRBase | Archive of miRNA sequences and annotations | A, P | 2004–14 | 2018 | v22 | WB | http://www.mirbase.org/ | [22] |
| HMDD | Human miRNA disease database | A | 2008–14 | 2014 | v2.0 | WB | http://210.73.221.6/hmdd | [69] |
| Bowtie | Short-read aligner | A, P | 2009 | 2017 | v1.2.2 | SA | http://bowtie-bio.source forge.net | [80] |
| mirPath | miRNA pathway analysis | A | 2009–15 | 2015 | v3.0 | WB | http://snf-515788.vm.okeanos.grnet.gr/ | [126] |
| miR2Disease | Human miRNA disease database | A | 2009 | 2008 | - | WB | http://www.mir2disease.org/ | [119] |
| ExoCarta | Exosome miRNA database | A | 2009–16 | 2015 | - | WB | http://www.exocarta.org/ | [76] |
| SeqBuster | Pipeline for the analysis of miRNA-Seq data set | A | 2010–16 | 2016 | v1.2.1 | SA | https://pypi.org/project/seqcluster/ | [127] |
| TransmiR | A database of transcription factor-miRNA regulations | A, P | 2010 | 2013 | v1.2 | WB | http://www.cuilab.cn/transmir | [103] |
| dbDEMC | A database of differentially expressed miRNAs in cancers | A | 2010–17 | 2017 | v2.0 | WB | http://www.picb.ac.cn/dbDEMC | [128] |
| starBase | Pan-Cancer ceRNA database | A | 2011–14 | 2013 | v2.0 | WB | http://starbase.sysu.edu.cn/ | [73] |
| miTALOS | miRNA pathway analysis | A | 2011–16 | 2016 | v2 | WB | http://mips.helmholtz-muenchen.de/mitalos | [129] |
| miRStart | A database of miRNA TSSs | A | 2011 | 2011 | - | WB | http://mirstart.mbc.nctu.edu.tw/ | [102] |
| miRandola | A database of circulating miRNA | A | 2012–17 | 2017 | v2017 | WB | http://mirandola.iit.cnr.it/ | [75] |
| miRNEST | Integrative resource of miRNA-associated data | A, P | 2012–14 | 2014 | v2.0 | WB | http://rhesus.amu.edu.pl/mirnest/copy/ | [123] |
| miR_editing | Scripts for detecting editing sites in miRNA-Seq data set | A | 2012–13 | 2013 | - | SA | http://www.tau.ac.il/∼elieis/miR_editing | [130] |
| ChIPBase | A database of transcription factor–miRNA regulations | A | 2013–17 | 2016 | v2.3.4 | WB | http://rna.sysu.edu.cn/chipbase/ | [122] |
| SM2miR | A database of the association between miRNA and small molecules | A | 2013 | 2015 | - | WB | http://210.46.85.180:8080/sm2mir/index.jsp | [120] |
| YM500 | Database for miRNA-Seq in human cancer research | A | 2013–17 | 2017 | v3 | WB | http://driverdb.tms.cmu.edu.tw/ym500v3/ | [150] |
| isomiRex | Web platform for isomiR identification | A, P | 2013 | 2013 | - | WB | http://bioinfo1.uni-plovdiv.bg/isomiRex/ | [99] |
| PHDcleav | Dicer cleavage sites predictor | A | 2013 | 2013 | - | WB | http://crdd.osdd.net/raghava/phdcleav/ | [58] |
| PASmiR | A database for miRNA molecular regulation in plant abiotic stress | P | 2013 | 2015 | - | WB | http://pcsb.ahau.edu.cn:8080/PASmiR | [70] |
| microTSS | miRNA TSS identification scripts | A | 2014 | 2014 | v1.0 | SA | http://www.microrna.gr/microTSS/ | [101] |
| Chimira | Web platform for miRNA modifications detection | A, P | 2015 | 2017 | v1.5 | WB | http://wwwdev.ebi.ac.uk/enright-dev/chimira/ | [161] |
| MirGeneDB | Curated miRNA gene database | A | 2015 | 2018 | v2.0 | WB | http://mirgenedb.org/ | [159] |
| DREAM | Web platform for detecting RNA editing association with miRNAs | A | 2015 | 2015 | - | WB | http://www.cs.tau.ac.il/∼mirnaed/ | [160] |
| IsomiR Bank | A database for tracking isomiRs | A, P | 2016 | 2016 | - | WB | http://mcg.ustc.edu.cn/bsc/isomir/ | [151] |
| TissueAtlas | Tissue specificity miRNA database | A | 2016 | 2016 | - | WB | https://ccb-web.cs.uni-saarland.de/tissueatlas/ | [152] |
| miRNAme Converter | miRNA ID converter | A, P | 2016 | 2018 | v1.8.0 | WB, SA | http://163.172.134.150/miRNAmeConverter-shiny | [149] |
| mirSTP | miRNA TSS tracking program | A | 2017 | 2017 | - | SA | http://bioinfo.vanderbilt.edu/mirSTP/ | [49] |
| ParSel | Web platform for predicting survival associated miRNA | A | 2017 | 2017 | - | SA | https://github.com/debsin/ParSel | [153] |
| isomiR2 Function | Integrated workflow for identifying isomiRs in plants | P | 2017 | 2017 | - | SA | https://github.com/347033139/isomiR2Function | [162] |
| PceRBase | Plant ceRNA database | P | 2017 | 2016 | - | WB | http://bis.zju.edu.cn/pcernadb | [74] |
| miRsig | Pan-cancer miRNA-miRNA interaction database | A | 2017 | 2017 | - | WB | http://bnet.egr.vcu.edu/miRsig/ | [154] |
| OncomiR | Web platform for exploring pan-cancer miRNA dysregulation | A | 2017 | 2017 | - | WB | http://www.oncomir.org/ | [155] |
Note: Organism: Animal (A), plant (P); Platform: Stand-alone (SA), Web-based (WB).