Semantics and Ambiguity of Stochastic RNA Family Models

My second interest are genome-wide scans for non-coding RNA. As Infernal (algorithms) and Rfam (database) are the two most widely used tools for this task, most of our work involves them. In Giegerich and Höner zu Siederdissen (2011), we investigated the ambiguity problem as it relates to Infernal and gave pointers toward new grammars and algorithms to increase the sensitivity of Infernal.

Discriminatory Power of RNA families: CMcompare

The quality of the Rfam database, escpecially the specifity of individual models were the topic of Höner zu Siederdissen and Hofacker (2010) which, in addition, provides an algorithm to check if newly developed models are “sufficiently far away” from existing models as, otherwise, one could expect to see several models “hit” the same locus in a genome. This kind of ambiguity should be avoided by Rfam models, but several hundred of the 1500 investigated models have low discriminatory power with regard to some other models.

CMcompare: Discriminatory Power of RNA Family Models

Non-Coding RNA families (Rfam)

The practical side of non-coding RNA searches are the biological RNA families. In Marz et al. (2011) we studied a small number of animal snoRNAs and scaRNAs and tried to improve the existing models, as well providing some new results on their (sometimes strange) structure.

local list of references

Robert Giegerich, and Christian Höner zu Siederdissen. 2011. Semantics and Ambiguity of Stochastic RNA Family Models. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8, no. 2. 8: 499–516. doi:10.1109/TCBB.2010.12.

Christian Höner zu Siederdissen, and Ivo L. Hofacker. 2010. Discriminatory power of rna family models. Bioinformatics 26, no. 18. 26: 453–59. doi:10.1093/bioinformatics/btq370.

Manja Marz, Andreas R. Gruber, Christian Höner zu Siederdissen, Fabian Amman, Stefan Badelt, Sebastian Bartschat, Stephan H. Bernhart, Wolfgang Beyer, Stefanie Kehr, Ronny Lorenz, Andrea Tanzer, Dilmurat Yusuf, Hakim Tafer, Ivo L. Hofacker, and Peter F. Stadler. 2011. Animal snoRNAs and scaRNAs with exceptional structures. RNA Biology 8, no. 6. 8: 1–9. doi:10.4161/rna.8.6.16603.