Site-prediction accuracy on 17 Drosophila developmental enhancers.

Results from rMONKEY on the 10-way alignments are missing because the program does not process the longer sequences due to large (>8 GB) memory requirements. All numbers are percentages. [“EMMA-E” results were obtained by running EMMA in a nonstandard configuration (command line option “-e”), which forces prior densities to be re-estimated on the test sequence. We included them here for completeness as they led to a noticeable improvement at least on this set of enhancers.]