Structure prediction of UnaL2 LINE 3' element

Comparison of the NMR derived reference (Rfam) structure of UnaL2 LINE 3' element and predicted structures. Using the original hamming distance covariance scoring of RNAalifold, the stem is not correctly predicted. This is due to a small number of counter examples in some of the base pairs of the stem (shown in pale below).

The RIBOSUM variant of RNAalifold predicts the main stem correctly, and is only wrong in the prediction of where the bulges are at the bottom of the stem.

Reference Structure of UnaL2 LINE 3' element	Reference Alignment of UnaL2 LINE 3' element
Structure using the original `RNAalifold`	Alignment of UnaL2 LINE 3' element original `RNAalifold` structure
Structure using RIBOSUM `RNAalifold`	Alignment of UnaL2 LINE 3' element RIBOSUM `RNAalifold` structure

Structure prediction of UnaL2 LINE 3' element

Reference Structure of UnaL2 LINE 3' element

Reference Alignment of UnaL2 LINE 3' element

Structure using the original `RNAalifold`

Alignment of UnaL2 LINE 3' element

original `RNAalifold` structure

Structure using RIBOSUM `RNAalifold`

Alignment of UnaL2 LINE 3' element

RIBOSUM `RNAalifold` structure

Structure prediction of UnaL2 LINE 3' element

Reference Structure of UnaL2 LINE 3' element

Reference Alignment of UnaL2 LINE 3' element

Structure using the original RNAalifold

Alignment of UnaL2 LINE 3' element

original RNAalifold structure

Structure using RIBOSUM RNAalifold

Alignment of UnaL2 LINE 3' element

RIBOSUM RNAalifold structure

Structure using the original `RNAalifold`

original `RNAalifold` structure

Structure using RIBOSUM `RNAalifold`

RIBOSUM `RNAalifold` structure