R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
Bottom Line: In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures.A web-based front end is available for manual entry and an Application Program Interface for programmatic access.Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range.
Affiliation: Institute for Cellular and Molecular Biology, and the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.Show MeSH
Related in: MedlinePlus
Mentions: Human-readable HTML output can be obtained from the server either by entering the desired nucleotide ranges manually on the input page or by providing the URL that encodes the search. The output web page contains three major components: (i) the ‘Query Information’ component, a summary of the query, (ii) a ‘Sequence Summary’ table listing the distinct sequence variants found in the alignment and (iii) a ‘Sequence Details’ table providing information for each sequence returned and its biological source. Figures 4 and 5 present a portion of the results from the sample query in Figure 3.
Affiliation: Institute for Cellular and Molecular Biology, and the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.