BMC Genomics 2005, 6:88 http://www.biomedcentral.com/1471-2164/6/88 ingTargets software program to provide a tool for the accu- rate and flexible prediction of miRNA targets in Drosophila. Using this tool, we identified a set of 83 high- likelihood miRNA targets. We tested and verified 3 of these predictions, including a target for the Drosophila let- 7 homolog. MovingTargets provides flexibility in describing the char- acteristics defining a miRNA target. Thus, as the rules gov- erning miRNA-target interactions are better elucidated, these constraints can be enforced through MovingTargets to produce more refined sets of miRNA target predictions. We used this flexibility to relax the constraints placed on a miRNA-target interaction to predict and validate miR- NAs targeting tramtrack. MovingTargets is freely available on DVD by request. Availability and Requirements The MovingTargets software is available on DVD by request. It can be used on any Perl platform, such as the Macintosh 'Terminal' utility. Usage of the software requires only minimal computer skills. The researcher can specify the biological constraints for a miRNA target search through the user interface. In addition, the researcher can specify a single target for focused searches with individual mRNAs. For a miRNA target search of the entire target database, the program runs in about 2 hours on an earlier generation Macintosh computer (466 MHz G4); focused searches for miRNAs targeting an individual mRNA are much faster and take about 20 minutes. List of abbreviations miRNA microRNA UTR untranslated region RNAi RNA interference RISC RNA-induced silencing complex PCR polymerase chain reaction DNA deoxyribonucleic acid RT room temperature FBS fetal bovine serum D. melanogaster Drosophila melanogaster D. pseudoobscura Drosophila pseudoobscura BDGP Berkeley Drosophila Genome Project mRNA messenger RNA Authors' contributions CB designed and implemented the software, performed all of the experiments and drafted the manuscript. CB and PMM together conceived of the study, and PMM helped to draft the manuscript Acknowledgements We thank the Texas Advanced Computing Center for use of computing resources, Takao Imai and Carl Thummel for plasmids, John Sisson for S2 cells and advice about their culture and use, and Robin Gutell and Rick Rus- sell for discussions. Supported by NIH grant GM54409. References 1. Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297. 2. 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