Algorithm and analysis pipeline. Source data consisting of (a) miRNAs and (b) 3' UTRs are processed initially by (c) the miRanda algorithm, which searches for complementarity matches between miRNAs and 3' UTRs using dynamic programming alignment (Phase 1) and thermodynamic calculation (Phase 2). (d) All results are then post-processed by first filtering out results not consistently conserved according to target sequence similarity with D. pseudoobscura and A. gambiae (Phase 3), then by sorting and ranking all remaining results. (e) Finally, all miRNA target gene predictions are annotated using data from FlyBase and stored for further analysis.
Enright et al. Genome Biology 2003 5:R1 doi:10.1186/gb-2003-5-1-r1