The DIANA-microT 3.0 algorithm. (a) A schematic overview of the algorithm. The miRNA driver sequence is mapped onto a 9 nt length window that slides along the 3'UTR sequence. The binding category of the driver:MRE interaction is defined by the number of binding nucleotides between the two sequences. G:U wobble pairs or less than 7 consecutive WC matches are only allowed if the free binding energy of the miRNA:MRE heteroduplex is under a binding category specific threshold (lower free binding energy corresponds to stronger binding). MREs are scored according to their binding category and degree of conservation in other species. The final miTG score is the weighted sum of all MREs on the miTG. (b) The top sequence (MRE) is part of the 3'UTR of a gene. The nine nucleotide region near the 5'end of the miRNA is called the driver sequence of the miRNA (shown in red). Sequences on the MRE, corresponding to positions 1-6, 2-7 and 3-8 from the miRNA 5'end are called anti-seed 1, anti-seed 2 and anti-seed 3 respectively. (c) An example of the miTG score calculation. The top line represents the 3'UTR sequence of a human gene containing three MREs with different conservation levels. Individual MRE scores are calculated depending on the degree of conservation of the MRE, and multiplied by a weight depending on the MRE binding category. The sum of all weighted MRE scores defines the final miTG score.
Maragkakis et al. BMC Bioinformatics 2009 10:295 doi:10.1186/1471-2105-10-295