The European database on small subunit ribosomal RNA

Abstract

The European database on SSU rRNA can be consulted via the World WideWeb at http://rrna.uia.ac.be/ssu/ and compiles all complete or nearly complete small subunit ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also available.

Figure 1

Scheme of the secondary structure of SSU rRNA. The core of the structure common to SSU rRNAs of Archaea, Bacteria and most Eucarya is drawn in black. Helices are numbered in the order of occurrence of their 5′-strand when following the chain from 5′- to 3′-terminus. They bear a different number when separated by a multibranched loop, a pseudoknot loop or a single-stranded area not forming a loop. Bulge loops and internal loops are not shown. Coloured helices are present in Archaea and Bacteria (green), in Bacteria only (blue) or in Eucarya only (red). Those drawn as solid red bars are present in all Eucarya with the exception of the protist taxa Microsporidia, Diplomonadida and Parabasalidea, where some of these helices and even some core helices can be absent. Those drawn as parallel red lines are present only in certain eukaryotic taxa. A helix is numbered N/en if it is the nth Eucarya-specific (red) helix following the 5′-strand of the Nth common core (black) helix. It is numbered N\en if it follows the 3′-strand of the Nth helix. Analogous nomenclature, N/bn and N\bn, is used for Bacteria-specific helices, N/abn and N\abn for those common to Archaea and Bacteria.