Stefan Washietl & Ivo L. Hofacker

Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics

J. Mol. Biol. 2004 342(1):19-30

Supplementary Material
  1. Perl scripts
  2. Rfam test sets
  3. SRP RNA: structural vs. ClustalW alignments
  4. Saccharomyces test set
  5. C. elegans/C. briggsae test set

Download the complete set of supplements: supplements.tar.gz

Note: Encouraged by the results described here, we have been working on an alternative (and faster) strategy for detecting ncRNAs based on consensus folding. This resulted in our new Program RNAz (http://www.tbi.univie.ac.at/~wash/RNAz). The method is described in Proc. Natl. Acad. Sci. U.S.A. 102, 2454-2459

1. Perl scripts

2. Rfam test sets

3. SRP RNA: structural vs. ClustalW alignments

All 2083 pairwise alignments of 73 eukaryotic SRP RNAs:

4. Saccharomyces test set

Note: Here are only shown some examples of S.cerevisiae ncRNAs (not all described in the paper).

Sequence data from saccharomyces species is taken from the Saccharomyces genome database. Abbreviations used:

The genomic coordinates for the S. cerevisiae sequences are given in the alignment (rc means reverse complement). The chromosome number is part of the file name:

5. C. elegans/C. briggsae test set

Sequences are specified by their GenBank accession number or their Wormbase identifier:


Stefan Washietl
Last modified: Mon Jul 31 11:09:29 CEST 2006