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.
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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.
PLEXY: Efficient Target Prediction for Box C/D snoRNAs
Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler and Hakim Tafer
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Status: Published
Bioinformatics (2011) 27 (2): 279-280
Abstract
Motivation: Small nucleolar RNAs (snoRNAs) are an abundant
class of non-coding RNAs with a wide variety of cellular functions
including chemical modification of RNA, telomere maintanance, prerRNA
processing, and regulatory activities in alternative splicing. The
main role of box C/D snoRNAs is to determine the targets for 2’-
O-ribose methylation, which is important for rRNA maturation and
splicing regulation of some mRNAs. The targets are still unknown,
however, for many “orphan” snoRNAs. While a fast and efficient target
predictor for box H/ACA-RNA target is available, no comparable tool
exists for C/D-Box snoRNAs, even though they bind to their targets in
a much less complex manner.
Results: PLEXY is a dynamic programming algorithm that computes
thermodynamically optimal interactions of a box C/D snoRNA with
a putative target RNA. Implemented as scanner for large input
sequences and equipped with filters on the duplex structure, PLEXY
is an efficient and reliable tool for the predictions of box C/D snoRNA
target sites.
Keywords
PLEXY, snoRNA, target prediction