Summary of bioinformatic tools that can be used to predict bacterial RNA-human RNA targets
| Tool | Uses energy* | Uses accessibility | Homology/ Conservation | Reference | GitHub or website link |
| Rfam | ✓ | 43 | https://rfam.xfam.org | ||
| BLAST | ✓ | 89 | https://blast.ncbi.nlm.nih.gov/Blast.cgi | ||
| RNAhybrid | ✓ | 46 | https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid?id=rnahybrid_view_submission | ||
| RNAnue | ✓ | ✓ | 53 | https://github.com/Ibvt/RNAnue | |
| RNAup | ✓ | ✓ | 23 | https://www.tbi.univie.ac.at/RNA/RNAup.1.html | |
| RNAplex | ✓ | ✓ | 24 | https://www.tbi.univie.ac.at/RNA/RNAplex.1.html | |
| IntaRNA | ✓ | ✓ | 22 27 | http://rna.informatik.uni-freiburg.de/IntaRNA/Input.jsp;jsessionid=41FFC5A7C2ED917ED3C204B6E3D9CB6B | |
| RIsearch2 | ✓ | ✓ | 47 | http://rth.dk/resources/risearch | |
| DGE and Correlation Analysis | 55 56 | – | |||
| IPA (TargetScan) | ✓ | 59 62 | https://www.qiagen.com/us/products/discovery-and-translational-research/next-generation-sequencing/informatics-and-data/interpretation-content-databases/ingenuity-pathway-analysis/ | ||
| miRanda | ✓ | ✓ | 64 | http://cbio.mskcc.org/miRNA2003/miranda.html | |
| DIANA-microT | ✓ | ✓ | 66 | https://diana.e-ce.uth.gr/home |
*Negative energy is associated with a higher likelihood of the interaction taking place.
DGE, differential gene expression; IPA, ingenuity pathway analysis.