SSU Java Secondary Structure Prediction Viewer for RDP

This is a Java viewer for two dimensional structure.

The top window is a two dimensional figure. The bottom window is an alignment of E.coli with your sequence. Click on a base in either window to highlight it.

The diagram is based on the canoncial E.coli structure. All SSU rRNA structures are shown as mutations, insertions, and deletions from this structure.

Colors give information about the type of deviation in structure.

blue is basepair that corresponds to a basepair in E.coli (helix match/mutation)
black is loop position that corresponds to a loop posotion in E.coli (loop match/mutation)
red is a basepair that occurs in E.coli but not your sequence (helix deletion)
yellow is loop position that occurs in E.coli but not your sequence (loop deletion)
green indicates structure in your sequence that is not in E.coli (insertion)

Note that in the alignment inserted structures (green) can contain inserted basepairs (basepairs in your sequence but not in E.coli) that are colored cyan.

These colors allow you to quickly see how your structure differs from the canonical E.coli structure.