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.
Highlights
Structured RNA molecules, like most proteins, owe their functions to the unique three-dimensional (3D) structure(s) that they form
The discovery of the nucleic acid double helical structure implied the geometric similarity, or ‘isostericity’, of the cis Watson–Crick (WC) basepairs (AU, UA, GC and CG) and suggested that compensating nucleotide changes at positions forming WC pairs preserve the helical structure and are generally neutral with regard to function. These ideas concerning RNA sequence variation of helical regions were applied in the 1960s to compare and align a handful of sufficiently divergent transfer RNA sequences to deduce a common set of WC basepairs shared by all members of the tRNA family, i.e. the well-known ‘cloverleaf’ secondary (2◦) structure
Since the 5.8S ribosomal RNAs (rRNAs) molecule found in eukaryotes is homologous to the 5’-end of the long LSU rRNA of bacterial, archaeal and organellar ribosomes, it is treated as part of the eukaryal LSU and its sequences are included in the LSU alignment
Summary
Structured RNA molecules, like most proteins, owe their functions to the unique three-dimensional (3D) structure(s) that they form. The discovery of the nucleic acid double helical structure implied the geometric similarity, or ‘isostericity’, of the cis Watson–Crick (WC) basepairs (AU, UA, GC and CG) and suggested that compensating nucleotide changes at positions forming WC pairs preserve the helical structure and are generally neutral with regard to function. These ideas concerning RNA sequence variation of helical regions were applied in the 1960s to compare and align a handful of sufficiently divergent transfer RNA (tRNA) sequences to deduce a common set of WC basepairs shared by all members of the tRNA family, i.e. the well-known ‘cloverleaf’ secondary (2◦) structure. The comparative sequence approach was subsequently extended to the 5S, 16S and 23S ribosomal RNAs (rRNAs) to accurately determine their WC pairings (2◦ structure) and some of the long-range pairs forming ‘pseudo-knots’, long before their 3D structures became available [1]
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