Table 2.
List of the most common databases and algorithms for predicting miRNA binding sites together with the organisms for which the prediction can be browsed (by sequence and/or by gene ID) and if they share the standalone version.
| Tool | Website | Organisms | Browse by Sequenc/Gene ID | Standalone Version |
|---|---|---|---|---|
| STarMir | http://sfold.wadsworth.org/cgi-bin/starmirtest2.pl | Human Mouse Worm Other |
Sequence/ Gene ID |
no |
| STarMirDB | http://sfold.wadsworth.org/starmirDB.php | Human Mouse Worm |
Gene ID | no |
| PITA | https://genie.weizmann.ac.il/pubs/mir07/index.html | Human Mouse Fly Worm |
Gene ID | yes |
|
miRanda/
mirSVR |
http://www.microrna.org/microrna/home.do | Human Mouse Rat Fly Worm |
Gene ID | yes |
| TargetScan | http://www.targetscan.org/vert_72/ | Human Mouse Fly Worm Zebrafish |
Gene ID | yes |
| RNAhybrid | https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid/ | Any | Sequence | yes |
| TarBase v8 | http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php | Human Mouse Rat Chicken Zebrafish Fly Worm Chimpanzees Macaque Soy Maize Barrelclover Grape wine Earthmoss Epstein–Barr virus KSHV |
Gene ID | no |