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 (
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) 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.
<tt>RNAsnoop</tt>: efficient target prediction for box H/ACA snoRNAs. Submitted.
Hakim Tafer, Stephanie Kehr, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler
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Status: Published
Bioinformatics. 26: 610-616 (2010)
Abstract
<b>Motivation:</b>
all nucleolar RNAs are an abundant class of non-coding RNAs that
guide chemical modifications of rRNAs, snRNAs, and some mRNAs. In the
case of many "orphan" snoRNAs, the targeted nucleotides remain
unknown, however. The box H/ACA subclass determines uridine residues
that are to be converted into pseudouridines via specific complementary
binding of in a well-defined secondary structure configuration that
is outside the scope of common RNA (co-)folding algorithms.
<br>
<b>Results:</b> implements a dynamic programming algorithm that
computes thermodynamically optimal H/ACA-RNA interactions in an
efficient scanning variant. Complemented by an SVM-based
machine-learning approach to distinguish true binding sites from
spurious solutions and a system to evaluate comparative information,
it presents an efficient and reliable tool for the prediction of H/ACA
snoRNA target sites. We apply <tt>RNAsnoop</tt> to identify the snoRNAs
that are responsible for several of the remaining ``orphan''
pseudouridine modifications in human rRNAs, and we assign a target to
one of the five orphan H/ACA snoRNAs in <e>Drosophila</e>.
<br>
<b>Availability:</b>
The C source code of <tt>RNAsnoop</tt> can be obtained under
the GPL from <a href="http://www.tbi.univie.ac.at/~htafer/RNAsnoop"><tt>http://www.tbi.univie.ac.at/~htafer/RNAsnoop</tt></a>
<tt>RNAsnoop</tt>
Note
doi:10.1093/bioinformatics/btp680