| "RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction. |
| Searching the minimum free energy hybridization of two desired RNA sequences |
| miRNA_Targets implemented well establised miRNA target prediction algorithms miRanda and RNAhybrid on mRNA 5 prime UTR's , coding regions and 3 prime UTR's. MicroRNA target predictions using 2 algorithms on 7 genomes. Versatile search capabilities using miRNA or mRNA individually or in groups. Gene ontology classification of sets of target genes. Visualization of miRNA and target gene location network on chromosomes. |
| Interaction prediction of a desired sequence and known miRNAs Target prediction using miRanda and RNAhybrid algorithms on mRNA 5´ UTR's , coding regions and 3´ UTR's |
| PITA devise a parameter-free model for microRNA-target interaction that computes the difference between the free energy gained from the formation of the microRNA-target duplex and the energetic cost of unpairing the target to make it accessible to the microRNA. This model explains the variability in our experiments, predicts validated targets more accurately than existing algorithms, and shows that genomes accommodate site accessibility by preferentially positioning targets in highly accessible regions. |
| Assessment of interactions between RNA sequences based on PITA algorithm Using known miRNAs or user-provided miRNA sequences |
| RNA22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. RNA22 does not rely upon cross-species conservation, is resilient to noise, and, unlike previous methods, it first finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA. |
| Identifying microRNA binding sites and their corresponding heteroduplexes Interaction prediction between a desired miRNA and target sequence |
| Single resource target prediction |
| "IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions. |
| Prediction of interactions between two RNA molecules |
| MIRZA is a biophysical model of miRNA-target interaction and infer its parameters from Argonaute 2 cross-linking and immunoprecipitation data. We show that a substantial fraction of human miRNA target sites are noncanonical and that predicted target-site affinity correlates well with the extent of target destabilization. |
| A biophysical miRNA-mRNA interaction model based on Argonaute 2 cross-linking and immunoprecipitation data |
| MR-microT is a MapReduce-based implementation of microT target prediction method. It provides near-real time predictions for custom miRNA sequences. MR-microT offers the highly requested by life scientists feature of predicting the targets of ad-hoc miRNA molecules in near-real time through an intuitive Web interface. |
| Provides near-real time predictions for custom miRNA sequences |
| psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: reverse complementary matching between miRNA and target transcript using a proven scoring schema, and target site accessibility evaluation by calculating unpaired energy required to open secondary structure around miRNA’s target site on mRNA. PsRNATarget distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript |
| Reverse complementary matching between miRNA and target transcript using a proven scoring schema Target site accessibility evaluation by calculating unpaired energy |
| TAPIR is designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA-target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA-target duplex having a large loop, making them undetectable by traditional tools. |
| Search for plant miRNA targets using a fast and a precise algorithm User defined score and free energy ratio |
