RNA 3D Structure-to-Multiple Sequence Alignment Server

A joint initiative of the BGSU RNA Group and the Comparative RNA Web (CRW) Project

Purpose: To link RNA 3D structures with high-quality sequence alignments. R3D-2-MSA enables users to select nucleotides from representative RNA 3D structures and seamlessly access sequence variants from large and diverse sequence alignments.

Examples

How to Use

  • First, select a reference 3D structure from PDB/NDB. Each entry in the menu is annotated with its organism and general structure contents.
  • Then, select an alignment. Structures that contain multiple RNAs will show more than one alignment as options.
  • Next, provide up to five nucleotide ranges of 1-50 nucleotides, using the nucleotide numbers from the structure.
    • For ranges of one nucleotide, only the "Start" position is required.
    • The "Start" position must be 5' to the "Stop" position.
    • Use the "+" button to add another range, and the "-" button to remove all ranges below that point.
    • Ranges may be entered in any order.
  • Submit your query.
  • For examples, click the example buttons.

Data Source

Representative alignments from the CRW Site (reference).