Comparative Detection of Processed Small RNAs in Archaea

Enzymatic splicing in Archaeal tRNAs is guided by bulge- helix-bulge structural elements, while much less seems to be known about splicing in other small RNAs (sRNAs). We conduct a genome-wide anal- ysis of several archaeal genomes to identify putative BHB elements and compare our ndings with available RNA-seq data. We also provide an analysis of the viability of using pattern-based and stochastic structural scanning algorithms for in silico studies of the occurrence of BHB motifs. Furthermore, we comment on splicing motifs in other small RNAs, which mostly do not t the pattern of bulge-helix-bulge motifs. Appendix and supporting les available at: http://www.bioinf.uni-leipzig.de/publications/supplements/14-001

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