| Name | Description |
|---|---|
| TargetFinder | TargetFinder will computationally predict small RNA binding sites on target transcripts from a sequence database. This is done by aligning the input small RNA sequence against all transcripts, followed by site scoring using a position-weighted scoring matrix. |
| TAPIR | The TAPIR webserver predicts targets for plant miRNAs. Two different search modes are possible, corresponding to two different tabs of the web interface. The "Fast" mode is using the FASTA (1) search engine while the "Precise" mode is using the RNAhybrid (2) search engine. |
| TargetScan | TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites that match the seed region of each miRNA (Lewis et al., 2005). As options, predictions with only poorly conserved sites and predictions with nonconserved miRNAs are also provided. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing |
| Bowtie | Bowtie is an ultrafast, memory-efficient shortread aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. |
| miRanda | miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center. This software will be further developed under the open source model, coordinated by Anton Enright and Chris Sander |
| RNAhybrid | 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. |