Publications - Published papers
Please find below publications of our group. Currently, we list 565 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
RNAz 2.0: improved noncoding RNA detection
Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker and Peter F. Stadler
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Status: Published
Pac Symp Biocomput. 2010:69-79 (2010)
Abstract
RNAz is a widely used software package for de novo detection of structured noncoding RNAs in comparative genomics
data. Four years of experience have not only demonstrated the applicability of the approach, but also helped us to
identify limitations of the current implementation. RNAz 2.0 provides significant improvements in two respects: (1)
The accuracy is increased by the systematic use of dinucleotide models. (2) Technical limitations of the previous
version, such as the inability to handle alignments with more than six sequences, are overcome by increased training
data and the usage of an entropy measure to represent sequence similarities. RNAz 2.0 shows a significantly lower
false discovery rate on a dinucleotide background model than the previous version. Separate models for structural
alignments provide an additional way to increase the predictive power. RNAz is open source software and can be
obtained free of charge at: http://www.tbi.univie.ac.at/~wash/RNAz/
Keywords
RNA structure; noncoding RNA; structure conservation; comparative genomics; gene prediction
Note
http://www.tbi.univie.ac.at/~wash/RNAz/