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BIOINF 07-001: Computational RNomics of Drosophilids

Dominic Rose, Jörg Hackermüller, Stefan Washietl,
Sven Findeiß, Kristin Reiche, Jana Hertel,
Peter F. Stadler, Sonja J. Prohaska

Supplemental Material

• D. melanogaster ncRNA candidate sequences (p>0.5, fasta):
  all (6.9 Mb)      [2L (1.3 Mb) - 2R (1.1 Mb) - 3L (1.5 Mb) - 3R (1.7 Kb) - 4 (34 Kb) - X (1.5 Mb)]


• D. melanogaster ncRNA candidate coordinates (p>0.5, bed):
  all      [2L - 2R - 3L - 3R - 4 - X]


• D. melanogaster ncRNA candidate annotation (p>0.5):
  2L - 2R - 3L - 3R - 4 - X


• Browsing the RNAz hits:
  2L (7824 loci), 2R (6646 loci), 3L (8765 loci), 3R (10351 loci), 4 (196 loci), X (8700 loci)

  The custom annotation field of the above html tables comprises:

  • Overlap to known RNAs of reference genome ('known=')
  • Overlap to known CDS elements of reference genome ('knownCDS=')
  • A blast search against the Rfam ('Rfam=')
  • A blast search against the Noncode ('Noncode=')
  • A blast search against the miRBase ('miRBase=')
  • A blast search against the Noncode ('ncRNAdb=')
  • A blast search against the Flybase ('Flybase=')
  • Applying tRNAscan ('tRNAscan=')
  • Applying RNAmicro ('RNAmicro=')



• Complete WPGMA clustering tree in newick format: [here]
  It can be viewed with: http://pbil.univ-lyon1.fr/software/njplot.html


• PDF containing additional figures and tables

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dominic