The Berlin RNA Databank was initiated in 1977 when 13 prokaryotic and 23 eukaryotic 5S rRNA sequences were known (Erdmann, 1977). The BERLIN RNA DATABANK as of January, 1994, contains a total of 733 sequences of 5S rRNAs or their genes. It includes sequences from 44 Archaea, 309 eubacteria, 20 plastids, 6 mitochondria, 333 eukaryotes and 21 eukaryotic pseudogenes. The databank format used is the format of the EMBL nucleotide sequence data library complemented by a Sequence Alignment (SA) field including secondary structural information. In addition to the standard data base entries, we are also including the sequences in an aligned format introducing a standard numeration based on the sequence of Escherichia coli 5S rRNA. The secondary structural information is displayed according to the minimal 5S rRNA structural model (Specht et al., 1990/1991a/1991b). Figure 1 shows the overall alignment of all archaeal 5S rRNAs including secondary structure information. The secondary structures of all types of 5S rRNAs consist of five helices, named A to E, which are connected by loops designated as a to e as shown in Figure 2. The Helix D is best suited to distinguish between the five different 5S rRNA structural groups (Fig. 2). One group consists of eukaryotes, one of eubacteria including plastids and mitochondria. For Archaea we distinguish a total of three different groups, division I comprising Thermococcales, Thermoplasmatales, Methanobacteria and Halobacteria, division II (Eocyta) and the last group is represented by the single organism, Octopus Spring species I (Specht et al., 1990/1991a/1991b).
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