"Viruses" means that the viral genome from which a viral microRNA is derived.
The algorithm used to predict target mRNAs of viral miRNAs. Currently, vHot supports three algorithms including TargetScan, miRanda, and RNAhybrid.
TargetScan (Lewis et al., 2003) predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA by calculating thermodynamic free energy using RNAFold package (Hofacker, 2003). Predictions are ranked using site number, site type, and site context, which includes factors that influence target-site accessibility. Detailed information can be found at (http://genes.mit.edu/targetscan).
miRanda (Enright et al., 2003, John et al. 2004) uses sequence complementarity (using a position-weighted local alignment algorithm), free energies, and conservation of target sites to predict miRNA-mRNA interactions. Detailed information can be found at (http://www.microrna.org).
RNAhybrid (Rehmsmeier et al., 2004) is an extension of classical RNA secondary structure prediction software tools such as RNAfold (Hofacker, 2003) and Mfold (Mathews et al., 1999) for finding the minimum free energy hybridization of a long and a short RNA to predict target mRNA-miRNA interactions. For further information, please refer to (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid).
DIANA micro T 3.0 (Maragkakis et al., 2009) uses miTGs (miRNA target gene score) by combining conserved and non-conserved MRE (miRNA Recognition Element) score to predict miRNA-mRNA interactions. Detailed information can be found at (http://diana.cslab.ece.ntua.gr/).
PITA (Kertesz et al., 2007) uses difference between the binding free energy of the miRNA-target duplex structure and the energetic cost of unpairing the target-site nucleotides to predict miRNA-mRNA interactions. For further information, please refer to (http://genie.weizmann.ac.il/).
Select 'Intersection (default)' if you want to view the search results commonly predicted by all three algorithms.
Select 'Union' if you want to see the list of entire target mRNAs predicted by at least one algorithm (any of TargetScan, miRanda, and RNAhybrid).
The search results by miRanda and RNAhybrid can be limited by setting a MFE (Minimum Free Energy) threshold. MiRNA-mRNA duplexes are stabilized by free energy arising from base-pairing and base-stacking. In general, the lower the free energy is, the more stable the secondary structure of miRNA-mRNA duplex is. If you set a MFE threshold level, vHoT selects the miRNA-mRNA pairs whose MFEs are below the specified threshold and only shows the screened test results. The default value is determined by referring to the MFEs of miRNA-mRNA duplexes which are experimentally validated.
The search result by TargetScan can be restricted by setting a total context score threshold which is the sum of the site-type, 3' paring, local AU, and position contributions. If you set a score threshold, TargetScan selects out miRNA-mRNA pairs whose context scores are above the specified threshold. The default value is chosen by referring to the total context scores of miRNA-mRNA duplexes which are experimentally validated.
The search result by DIANA microT can be restricted by setting a score threshold. If you set a score threshold, DIANA microT selects out miRNA-mRNA pairs whose scores are above the specified threshold. The minimum (and default) value is 7.3.
The search results by PITA can be limited by setting a ddG threshold. If you set a ddG threshold score, vHoT selects the miRNA-mRNA pairs whose scores are below the specified threshold and only shows the screened test results. The default value is chosen by regarding the number of results taken into account.
Search speed can be improved by specifying gene names in query instead of searching the entire genome. Please enter a comma-separated list of mRNA accession IDs of interest in the box below. mRNA accession ID can be obtained from NCBI (http://www.ncbi.nlm.nkh.gov/).