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.
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.