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.
Target prediction and a statistical sampling algorithm for RNA-RNA interaction
Fenix Huang, Jing Qin, Christian M Reidys, Peter F Stadler
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Status: Published
Bioinformatics 26:175-181 (2010)
Abstract
Motivation It has been proven that the accessibility of the target
sites has a critical influence on RNA-RNA binding in general and
the specificity and efficiency of miRNAs and siRNAs in particular.
Recently, O(N6) time and O(N4) space dynamic programming
algorithms have become available that compute the partition function
of RNA-RNA interaction complexes, thereby providing detailed
insights into their thermodynamic properties.
Results:
Modifications to the grammars underlying earlier approaches
enables the calculation of interactions probabilities for any given
interval on the target RNA. The direct computation of the “hybrid
probabilities” is complemented by a stochastic backtracing algorithm
that produces samples from the Boltzmann ensemble of RNA-RNA
interaction structures. The sampling of k structures requires only
negligible additional memory resources and runs in O(k · N3).
Availability:
The algorithms described here are implemented in
C as part of the rip package. The source code of rip2
can be downloaded from http://www.combinatorics.cn/cbpc/rip2.html and http://www.bioinf.uni-leipzig.de/Software/rip.html.
Keywords
RIP, RIPhybrid, RNA-RNA interaction, target prediction
Note
http://www.combinatorics.cn/cbpc/rip2.html