Figure 2.

The Java-based VARNA-align program is automatically opened in user’s internet browser to render the secondary structure of the IRES being accessed or to render search results graphically as two structures. The user can interactively move parts of the structure, zoom in/out and perform several other actions. In the upper left corner, a complete c-myc IRES structure (IRESite_ID: 35) is shown in gray at low resolution. Its matching part (found by RNAforester) is shown below in the lower left corner, and the adjusted query structure is shown on the right side The RNAforester search mode used for searches through the IRESite is called ‘small-in-large’. Here, the query is treated by the RNAforester algorithm as a small structure, whereas the target structure is a large structure. Bases in black circles represent matching positions (primarily reflecting structural attributes and, to a lesser extent, nucleotides). Bases in gray circles are in the positions surrounding (outside) the matching region, and bases in red circles are in positions having no counterpart in the other structure (inside the matching region).