J. Mol. Biol. 2004 342(1):19-30Supplementary Material
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
Use the latest shuffle-aln.pl version. It comes with the option ``--mode conservative2'' which you can use to more efficiently shuffle alignments with many sequences or high divergence. See --help for details.
All 2083 pairwise alignments of 73 eukaryotic SRP RNAs:
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:
Sequences are specified by their GenBank accession number or their Wormbase identifier: