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:

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Customized strategies for discovering distant ncRNA homologs

Axel Mosig, Liang Zhu, Peter F. Stadler

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Brief. Funct. Genom. Proteom. 8(6):451-460

Abstract


Most non-coding RNAs are short and/or poorly conserved in sequence. Most of the longer examples, furthermore, consist of a collection of conserved structural motifs rather that a coherent globally conserved secondary structure. As a consequence, the conceptually simple problem of homology search becomes a complex and technically demanding task. Despite the best efforts of databases such as <tt>Rfam</tt>, the situation is complicated further by the sparsity of information on many - in particular prokaryotic - RNA families. In this contribution we review recent efforts to customize sequence-based search tools for ncRNA applications. In particular semi-global alignments and the development of methods for fragmented pattern search have brought significant practical advances. Current developments in this area focus on the integration of fragmented sequence pattern search with search algorithms for secondary structure patterns. As one example, we introduce here <tt>fragrep3</tt>.

Keywords


homology search, noncoding RNA, fragmented pattern, fragrep