Publications - Published papers

Please find below publications of our group. Currently, we list 563 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.

The tedious task of RNA homology search

Peter Menzel, Jan Gorodkin and Peter F. Stadler


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Status: Published

RNA 15:2075-2082 (2009)


User driven <em>in silico</em> RNA homology search is still a non-trivial task. In part this is the consequence of a limited precision of the computational tools in spite of recent exciting progress in this area, and to a certain extent computational costs are still problematic in practice. An important, and as we argue here, dominating issue is the dependence on good curated (secondary) structural alignments of the RNAs. These are often hard to obtain not so much because of an inherent limitation in the available data, but because they require substantial manual curation, an effort that is rarely acknowledged. Here, we qualitatively describe a realistic scenario for the what a ``regular user&#039;&#039; (i.e., a non-expert in a particular RNA family), can do in practice, and what kind of results are likely to be achieved. Despite the indisputable advances in computational RNA biology, the conclusion is discouraging: \prog{BLAST} still works better or equally good as other methods unless extensive expert knowledge on the RNA family is included. Homology search beyond the reach of BLAST hence is not at all a routine task.


RNA secondary structure prediction, non-coding RNA homology search, RNA structural alignments