Table 2. Some selected bioinformatic resources for microRNA (miRNA) target prediction.
| Group | Tools | Type | Organism(s) | Site coverage on mRNA | Input data | MRV | PER | USD | UA | UL | NTI | LU | URL | References | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P | 5′ UTR | CDS | 3′ UTR | ||||||||||||||
| Single platform | TargetScan | Web serverA | h, m, r, d, cn, c, rh, cw, o, fr, z, f, w | √ | GS, MF | 10.1, 17,21 | 69% spa | Y | N | A | - | 2015 Y | http://www.targetscan.org/ | (10,87,98) | |||
| RNAhybrid | Web server /softwareA | f, w | √ | TS, MS | - | 58% seb | Y | Y | Ad | - | 2006N | http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/ | (90,100) | ||||
| PicTar | Web serverNA | h, m, f, w | √ | MI, GI | 6 | 70% spa | N | N | A | - | 2007N | http://pictar.mdc-berlin.de/ | (99) | ||||
| rna22 | Web serverNA | h, m, f, w | √ | √ | √ | MS, TS, RT, MD | 16, 18, 19, 21 | 81% spa | Y | N | I | - | 2015Y | https://cm.jefferson.edu/rna22/ | (101,102) | ||
| PITA | Web server /softwareA | h, m, f, w | √ | MI, GI, US, MS | 11 | 0.76 AUC score | Y | Y | A | - | 2008N | http://genie.weizmann.ac.il/pubs/mir07/ | (103) | ||||
| miRDB | Database/web serverNA | h, m, r, d, cn | √ | √ | √ | MI, GI, GA, GS, MS, TS | 9.1, 10, 13, 18, 21 | - | Y | Y | A | - | 2015Y | http://mirdb.org/ | (88,104) | ||
| microRNA.org/Miranda | Database /softwareA | h, m, r, f, w | √ | MI, GS | 10, 11, 15 | 76% spa | Y | N | A | - | 2010Y | http://www.microrna.org/ | (105,184) | ||||
| DIANA-microT-CDS | Web server/softwareA | h, m, f, w | √ | √ | MI, GI, KD | 18 | 65% se | Y | N | A | - | 2013Y | http://www.microrna.gr/webServer | (107) | |||
| STarMir | Web serverNA | h, m, w | √ | √ | √ | MI, MS, GI, TS | 20 | - | Y | N | A | - | 2014Y | http://sfold.wadsworth.org/cgi-bin/starmirtest2.pl | (109) | ||
| Integrated platform | miRNAMap | DatabaseNA | h, m, r, d, cn, o, fr, z, f, w, p, mq | √ | MI, GI | 6, 9.2 | N | Y | A | 3 | 2008N | http://mirnamap.mbc.nctu.edu.tw/ | (185,186) | ||||
| MiRror/miRror Suite | DatabaseNA | h, m, r, f, w, z | √ | √ | √ | MI, GI | - | Y | Y | A | 15 | 2014Y | http://www.proto.cs.huji.ac.il/mirror/index.php | (187,188) | |||
| miRTar | Web serverNA | h | √ | √ | √ | MA, MS, GI,GS, PN | 15 | Y | Y | I | 4 | 2011Y | http://mirtar.mbc.nctu.edu.tw/human/ | (189) | |||
| miRWalk | DatabaseNA | h, m, r | √ | √ | √ | √ | GS, GI, MI,MA, PN,CT, OT, MT | 20 | Y | Y | A | 8 | 2015Y | http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/ | (190) | ||
| mirDIP | Web serverNA | - | √ | √ | √ | GS, MI | - | Y | Y | A | 12 | 2012Y | http://ophid.utoronto.ca/mirDIP/ | (95) | |||
| ComiR | Web serverA | h, m, f, w | √ | MI, TS | - | Y | Y | A | 4 | 2014Y | http://www.benoslab.pitt.edu/comir/ | (191) | |||||
| mirTarPri | Web serverNA | h | PD, MI | - | N | N | A | 6 | 2013Y | http://210.46.85.180:8080/mirTarPri/ | (192) | ||||||
| miRmap | Web server/softwareA | h, m, r, cw, o, cn, c, z | √ | MI, GS, TS | 19 | Y | Y | Ad | 4 | 2013Y | http://mirmap.ezlab.org/ | (193,194) | |||||
| ToppMiR | Web serverNA | h | MI, GS, GI | - | N | Y | Ad | 7 | 2014Y | https://toppmir.cchmc.org/ | (195) | ||||||
Type: Asource code available; NAnot available
Organisms: h, human; m, mouse; r, rat; d, dog; cn, chicken; c, chimpanzee; rh, rhesus; cw, cow; o, opossum; fr, frog; z, zebrafish; f, fly; w, worm; p, pufferfish; mq, mosquito
Input data: GS, gene symbol; MF, miRNA family; TS, target sequence; MS, miRNA sequence; RT, RNA type; MD, miRNA database; GA, GeneBank accecetion; MI, miRNA ID; GI, Gene ID; US, UTR sequence; KD, kegg descriptions, MA, miRBase accession number, PN, pathway name; CT, chromosome targets; OT, OMIM targets; MT, mitochondrial targets; PD, prediction database
MRV: miRBase release version
PER, performance: se, sensitivity; sp, specificity; AUC, area under the curve; a Ahmadi et al. (196), 2013; bZhang et al. (197)
USD, user submitted data: Yes (Y) or No (N); UA, user adjustability: Yes (Y) or No (N); UL, user level: all (A), advanced (ad), I (intermediate); NTI, no. of tools integrated; LU, last updated: Yif updated over the past 5 years, Nnot updated.