Flexible RNA Design with Partial Constraints

RNA design is increasingly shaped by practical questions: which parts of an RNA must be preserved, which can be changed, and how much freedom a design method should have to explore alternatives. Traditional RNA design approaches often require designers to fully specify their goals upfront, even when only partial knowledge about sequence or structure is available. In this chapter, we introduce partial RNA design, a new design paradigm that separates task formulation from sequence generation. Rather than demanding complete and rigid specifications, partial RNA design allows designers to express what matters, such as conserved motifs, structural elements, or sequence regions, while leaving remaining degrees of freedom open for computational exploration. This enables intuitive, flexible, and reusable design formulations that closely mirror real-world RNA engineering workflows. We then present libLEARNA as a practical tool that implements partial RNA design and generates diverse candidate RNA sequences consistent with the specified constraints. The chapter focuses on how partial RNA design tasks can be formulated and solved using libLEARNA, guiding readers from conceptual design ideas to concrete RNA sequence candidates.