RNAs play a major role in all living beings. RNAs are involved in translation and splicing, they can have catalytic as well as regulative function. For most of these processes the structure of the RNA molecule, not the sequence, is important. Therefor it is of much interest to know the structure of an RNA.

RNAs build structure by forming hydrogen bonds between complementary bases. As in DNA there are the Watson-Crick pairs C-G and A-U (remember that Uracil substitutes Thymin in RNA) and additionally we frequently find the Wobble pair G-U. But different from DNA the basepairs are not formed between two strands, but the RNA molecule folds back onto itself.

In this section, we will use several tools for:

• secondary structure prediction of RNAs
• comparative structure prediction
• RNA structure comparison