Publications - Supplemental material
Please find below supplemental material corresponding to publications of our group. Currently, we list 133 supplements.
If you have problems accessing electronic information, please let us know:
You may use this URL to cite or link to us.
©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/11-012You 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.
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
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
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!
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 INPUTThe 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 fileClick 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!