Showing papers by "Rupert De Wachter published in 1999"
TL;DR: The Antwerp database on large subunit ribosomal RNA now contains 607 complete or nearly complete aligned sequences, which incorporates secondary structure information for each sequence.
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/ CONTENTS OF THE DATABASE The Antwerp database on the structure of large subunit ribosomal RNA (LSU rRNA) provides an alignment of 607 sequences spanning a diverse range of taxonomic groups. The alignment is regularly updated and refined using a combination of automatic and manual methods, taking into account the knowledge of the structure model. Secondary elements are indicated in each sequence. New or updated rRNA sequences in the EMBL nucleotide sequence database (1) are scanned for rRNA sequences using the ‘Current Sequence Awareness’ service of the Belgian EMBNet node (http://ben.vub.ac.be ). Partial sequences are not included in
158 citations
TL;DR: A variability map of the eukaryotic large subunit ribosomal RNA is presented, showing the distribution of variable and conserved sites in this molecule, based on the SRC method, which provides a much more accurate and objective description of site-to-site variability.
Abstract: In this paper, we present a variability map of the eukaryotic large subunit ribosomal RNA, showing the distribution of variable and conserved sites in this molecule. The variability of each site in this map is indicated by means of a colored dot. Construction of the variability map was based on the substitution rate calibration (SRC) method, in which the substitution rate of each nucleotide site is computed by looking at the frequency with which sequence pairs differ at that site as a function of their evolutionary distance. Variability maps constructed by this method provide a much more accurate and objective description of site-to-site variability than visual inspection of sequence alignments.
58 citations