From this page you can download results from a preliminary scan for conserved secondary structure (presumed RNA genes or functional elements), running the PFOLD program over multiple alignments generated by the Pachter group.
These results were obtained using the default rate parameters for PFOLD, with a 200bp sliding window moved at 50bp increments. The following tree was estimated from one of the alignments using weighbor, and was used for all scans:
((DroVir_20040712:2.473067,((DroPse_1:0.974015,DroAna_20040713:0.899675):0.148856,DroMel_3_1:0.022465):0.128241):0.138872,DroYak_1:0.353634,DroEre_20041028:0.162208);
The scanning was done by this Perl script (pfoldscan.pl) and the results mapped back to genomic co-ords using this Perl script (scan2gff.pl).
The complete results, mapped back onto release 3.2 of the Drosophila melanogaster genome, can be downloaded here as a gzipped GFF file (warning: 50MB). For comparison, the 3.2.2 D.mel. annotation can be downloaded from here.
More questions? Contact Ian Holmes (ihh at berkeley dot edu) or see the Multiple-Fruitfly AAA (Assembly/Alignment/Annotation) page.