Publications - Published papers

Please find below publications of our group. Currently, we list 500 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 (access) 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


PREPRINT 10-032: [ PDF ]  [ Software ]


Bioinformatics (2011) 27 (2): 279-280


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.


PLEXY, snoRNA, target prediction