Database on the structure of large subunit ribosomal RNA

Abstract

The Antwerp database on large subunit ribosomal RNA now contains 607 complete or nearly complete aligned sequences. The alignment incorporates secondary structure information for each sequence. Other information about the sequences, such as literature references, accession numbers and taxonomic information is also available. Information from the database can be downloaded or searched on the rRNA WWW Server at URL http://rrna.uia.ac.be/

Phylogenetic relationship within the Erythrobasidium clade: Molecular phylogenies, secondary structure, and intron positions inferred from partial sequences of ribosomal RNA and elongation factor-1α genes

“…Secondary structures of the C1 helix (De Rijk et al, 1999) in 26S rRNA were predicted using the RNAfold Web interface on an online RNA folding server at URL http://rna.tbi.univie.ac.at/ cgi-bin/RNAfold.cgi (Hofacker, 2003). All analyses were performed on default parameters except for changing the temperature to 25°C.…”

“…The structural variation of the secondary structure of 26S rRNA was considered to be taxon specific among the eukaryotic taxa, and additional Eukarya-specific insertions in the universal helix C1 (De Rijk et al, 1999) were numbered from C1/e1 to C1/e6 (Wuyts et al, 2001). A sequence deletion shared among species of the three subgroups Bannoa, Erythrobasidium, and Sakaguchia was expected to occur in the C1 helices family.…”

Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences

“…Initial alignments of the 16S rRNA sequences were performed with Clustal X (Thompson et al, 1997) with default gap costs. Alignments were then refined by eye on the basis of 16S rRNA secondary structure (De Riijk et al, 1999). Most of cytochrome b gene sequences used in this study were downloaded from GenBank (see Table 2).…”

The Phylogenetic Relationships of the Suborder Acanthuroidei (Teleostei: Perciformes) Based on Molecular and Morphological Evidence

“…Sequence variation between species was compared against the original electropherograms as a further check on sequence quality. The aligned data were then exported as a NEXUS file and organized into stem and loop regions using models presented by Van de Peer et al (1994) and de Rijk et al (1994) for 12S and 16S mitochondrial DNA, respectively. Each stem was examined visually for base-pair complementarity and alignments in loops were adjusted where needed.…”