Figure 4.

Integrated sets of computer programs are a necessity for analyzing RNA sequences and structures as well as for modeling RNA structures by the assembly of identified modules. Details of the workflow of the Assemble package (http://bioinformatics.org/assemble). This application is divided into two main components: (1) a 3D panel rendering the 3D model and (2) a 2D panel displaying the secondary structure scaffold of this model. Because of their interconnections, the secondary structure is used as a guide during the modeling process. The secondary structure can be loaded or computed from several file formats or can be inferred from a dedicated tool like the S2S application (Jossinet and Westhof 2005).