Publications - Supplemental material

Please find below supplemental material corresponding to publications of our group. Currently, we list 114 supplements. If you have problems accessing electronic information, please let us know:

©NOTICE: All documents are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

This supplement is also available at http://www.bioinf.uni-leipzig.de/publications/supplements/11-012
You may use this URL to cite or link to us.

BIOINF 11-012: Protein-Coding Structured RNAs<br> A Computational Survey of Conserved RNA Secondary Structures Overlapping Coding Regions in Drosophilids

Sven Findeiß, Jan Engelhardt, Sonja J. Prohaska and Peter F. Stadler

The available files follow in principle the UCSC bed and gff format.

RNAz Data

The RNAz overview table with links to all loci and the underlying alignments is available here (p-value > 0.5) and here (p-value > 0.9).

Genome wide RNAz predictions p-value > 0.5: UCSC bed file   original RNAz file with loci and their correpsonding windows
Genome wide RNAz predictions p-value > 0.9: UCSC bed file   original RNAz file with loci and their correpsonding windows

RNAcode Data

System call: RNAcode -o OUTPUT.rcd --stop-early -p 0.05 INPUT
The coordinates in rcd files are zero based!

Genome wide RNAcode predictions full data set: UCSC bed file   gff file  original output file
Genome wide RNAcode predictions best only: UCSC bed file   gff file  original output file
Genome wide RNAcode predictions combined into cHSS if HSS was not further apart than 51 nt and in the same reading frame: UCSC bed file

RepeatMasker filtered and CDS removed cHSS: UCSC bed file

Complete UCSC Tracks

All tracks: one UCSC custom track bed file

Click here to load all RNAz and RNAcode UCSC tracks into the UCSC browser. Due to the huge amount of data this process may take a while!

Supplemental PDF

A detailed description of the used methods can be downloaded here.