R3DAID, pronounced "Red Aid" takes two chains from PDB representing the same molecule, aligns them using cmalign from Infernal and covariance models from Rfam, and displays the alignment visually by listing each pair of aligned nucleotides next to each other. Between the nucleotides is a bar that is colored according to the number of conserved basepairs made by the two nucleotides. Basepairs are indicated by colored arcs to the left and right of the alignment. Symmetrical arcs indicate that the alignment quality is good. After clicking Submit, the PDF may download directly to your computer, where it can be visualized using a tool like Adobe Acrobat Reader.
R3DAID is under construction as of 12/11/2024. Coloring, hiding, dimming, and turning off helix numbering are not yet implemented.
| Show | Dim | Hide | Interaction |
|---|---|---|---|
| nested Watson-Crick basepairs | |||
| non-nested Watson-Crick basepairs | |||
| nested non-Watson-Crick basepairs | |||
| non-nested non-Watson-Crick basepairs | |||
| stacking interactions | |||
| base-phosphate interactions | |||
| base-ribose interactions | |||
| near interactions |
Example 1
E. coli and T. thermophilus SSU rRNA; very good alignment and identical numbering by design; changes in helix length around E. coli number C188 and U209
are well known but lead to small deficiencies in the alignment.
Example 2
E. coli and S. aureus LSU rRNA
Example 3
E. coli and human SSU rRNA cross domain alignment; human has many insertions compared to E. coli
Example 4
human and yeast SSU rRNA
Example 5
H. marismortui and human 5S rRNA; note the scoring of the G-bulge at H.m. G78, U79.
Example 6
tRNAs