title: R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
abstract: The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. 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. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa.
authors.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.
authors.forename: Jamie J
authors.initials: JJ
authors.lastname: Cannone
authors.affiliation: Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
authors.forename: Blake A
authors.initials: BA
authors.lastname: Sweeney
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Anton I
authors.identifier: http://orcid.org/0000-0001-7279-2682
authors.initials: AI
authors.lastname: Petrov
authors.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.
authors.forename: Robin R
authors.initials: RR
authors.lastname: Gutell
authors.affiliation: Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA.
authors.forename: Craig L
authors.initials: CL
authors.lastname: Zirbel
authors.affiliation: Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA leontis@bgsu.edu.
authors.forename: Neocles
authors.initials: N
authors.lastname: Leontis
mesh_terms: D020407:Internet; D009690:Nucleic Acid Conformation; D012335:RNA, Ribosomal / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012335:RNA, Ribosomal