Publications - Published papers

Please find below publications of our group. Currently, we list 508 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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Non-Coding RNA Annotation of the Genome of <em>Trichoplax adhaerens</em>

Jana Hertel, Danielle de Jong, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater, Peter F. Stadler

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Nucleic Acids Res. 37: 1602-1615 (2009)

Abstract


A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of <em>Trichoplax adhaerens</em>, the presumably most basal metazoan whose genome has been published to-date. Since <tt>blast</tt> identified only a small fraction of the best-conserved ncRNAs --- in particular rRNAs, tRNAs, and some snRNAs --- we developed a semi-global dynamic programming tool, <tt>GotohScan</tt>, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the <em>Trichoplax</em> genome.

Keywords


<em>Trichoplax adhaerens</em>, non-coding RNA, genome annotation, homology search, spliceosomal RNAs, microRNAs

Note


doi:10.1093/nar/gkn1084