REAPR: realignment for prediction of structural non-coding RNA

Results and Data

The REAPR results, including our high-confidence predictions, and supplemental data are available for download as one comprehensive zip archive or as single files as listed below:

• High-confidence predictions in Drosophila melanogaster of REAPR, REAPR controls, RNAz, and EvoFold; dm2 coordinates
  • REAPR Delta 5, structure-based realignment within deviation 5 [reapr5_dm2.bed]
  • REAPR Delta 10, structure-based realignment within deviation 10 [reapr10_dm2.bed]
  • REAPR Delta 20, structure-based realignment within deviation 20 [reapr20_dm2.bed]
  • REAPR Initial, predictions from initial alignment without realignment [intial_dm2.bed]
  • REAPR Muscle, predicitons after realignment with Muscle [muscle_dm2.bed]
  • RNAz, RNAz 1.0 screen by Rose et al. [rnaz_dm2.bed]
  • EvoFold, EvoFold screen by Stark et al. (long and short predictions) [evofold_dm2.bed]
• High-confidence predictions in Homo sapiens ENCODE regions of REAPR, RNAz, EvoFold, and CMfinder; hg18 coordinates
  • REAPR Delta 20, structure-based realignment within deviation 20 [reapr20_hg18.bed]
  • RNAz, RNAz 1.0 screen by Washietl et al. [rnaz_hg18.bed]
  • EvoFold, EvoFold screen by Washietl et al. [evofold_hg18.bed]
  • CMfinder, CMfinder screen by Torarinsson et al. [cmfinder_hg18.bed]
• Table of all loci with RNAz scores and q-values in fly
  • REAPR Delta 5, structure-based realignment within deviation 5 [reapr5_loci.tab.zip]
  • REAPR Delta 10, structure-based realignment within deviation 10 [reapr10_loci.tab.zip]
  • REAPR Delta 20, structure-based realignment within deviation 20 [reapr20_loci.tab.zip]
  • REAPR Initial, predictions from initial alignment without realignment [intial_loci.tab.zip]
  • REAPR Muscle, predicitons after realignment with Muscle [muscle_loci.tab.zip]
• Table of all loci with RNAz scores and q-values in ENCODE
  • REAPR Delta 20, structure-based realignment within deviation 20 [reapr20_loci.tab]
  • REAPR Initial, predictions from initial alignment without realignment [intial_loci.tab]
  • REAPR Muscle, predicitons after realignment with Muscle [muscle_loci.tab]
• Drosophila Phylogeny We provide cooccurrences in high-confidence predictions and background cooccurrences in D. melanogaster by REAPR (Delta 20) for all pairs of fly species. In the following matrices, the columns and rows are labeled in alphabetical order of the 12 fly species names.
  • Background cooccurrences
  • Cooccurrences in high-confidence predictions

  The R-script phylogeny.R produces a Drosophila phylogeny from the above matrices.

  Furthermore, we report occurrences in high-confidence predictions and background.

  • Background occurrences
  • Occurrences in high-confidence predictions
• Embryonic Developmental Time Course analysis
• REAPR (Delta 20) predictions with transcription >= 100 and transcription profile [pdf] [table]
• REAPR (Delta 20) predictions with transcription >= 200 and transcription profile [pdf] [table]
• REAPR (Delta 20) predictions with transcription >= 400 and transcription profile [pdf] [table]
• REAPR (Delta 20) predictions with transcription >= 1000 and transcription profile [pdf] [table]
The pdfs are created from the tab files with the R-script profile.R.
• Annotations
  We provide the cleaned annotation sets for D. melanogaster that are used in the paper. All coordinates have been lifted to dm2.
  • Rfam [dmel-rfam-dm2.bed] derived from Rfam 10.0 seed alignments
  • FlyBase tRNA [dmel-tRNA-dm2.bed] derived from corresponding FlyBase dmel 5.40 annotation
  • FlyBase miRNA [dmel-miRNA-dm2.bed] derived from corresponding FlyBase dmel 5.40 annotation
  • FlyBase miscRNA [dmel-miscRNA-dm2.bed] derived from corresponding FlyBase dmel 5.40 annotation
  • FlyBase ncRNA [dmel-ncRNA-dm2.bed] derived from corresponding FlyBase dmel 5.40 annotation

Original Whole Genome Alignment

We provide the original whole genome alignment used in this study. We obtained the WGA from http://www.sanger.ac.uk/Users/td2/pecan-CAF1, following the citation of this URL in Rose et al.¹ However, this mirror no longer works, nor could we find alternative working mirrors.

¹ Rose, D., Hackermuller, J., Washietl, S., Reiche, K., Hertel, J., Findeiss, S., Stadler, P. F., and Prohaska, S. J., 2007. Computational RNomics of Drosophilids. BMC Genomics, 8:406.