MicroRNA sequences that are either experimentally confirmed or where there is strong bioinformatic evidence for their expression, can be obtained from the miRBase::Sequences resource at the Sanger Institute at http://www.sanger.ac.uk/Software/Rfam/mirna

Target candidate sequences can be downloaded from a variety of sources:

• The Ensembl database at http://www.ensembl.org
• For a bulk download of a large number of sequences, it is best to use Ensembl's MartView at http://www.ensembl.org/Multi/martview There you can also select sequences of 3'UTRs from a number of model organisms.
• For flies, an excellent resource is http://www.flybase.org
• For Arabidopsis, go to http://www.arabidopsis.org
• For other plant genomes (or eukaryotic genomes in general), have a look at http://www.tigr.org/tdb/euk
• If you are interested in worm genes, this is a good address: http://www.wormbase.org

In addition to RNAhybrid, there is a number of other miRNA target prediction methods, the majority of which, however, is not available as a tool. Instead, predicted miRNA/target interactions are presented on the web:

• Drosophila target prediction at EMBL at http://www.russell.embl.de/miRNAs
• The miRBase::Targets database at the Sanger Institute: http://microrna.sanger.ac.uk/targets. The core program (called miRanda) can also by downloaded from: http://www.microrna.org/miranda.html
• Human, fly, and zebrafish subsets of miRanda predictions at http://www.cbio.mskcc.org/mirnaviewer
• The PicTar database at http://pictar.bio.nyu.edu
• The TargetScan website at http: //genes.mit.edu/targetscan/index.html
• And RNAhybrid again, at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid