Figure 1.

An example of colored text output from a structure-based search through the secondary structures contained in the IRESite. These are recorded as a series of left and right brackets (paired bases) and dots (unpaired bases). The web site allows users to search by structural motif, optionally accompanied by the primary sequence. Our wrapper around the RNAforester program computes simple statistics for each result and displays the location of the hit within the target structure (numbers to the left/right of the alignment). Please note that position numbers are relative to the experimentally mapped secondary structure region, not to the mRNA sequence coordinates. Here, the hepatitis B virus encapsidation signal was used as a sample query that hit part of the synthetic KMI1 IRES structure with the best (highest) score. Adjustments to both the query and target made by RNAforester to yield the alignment are shown in red.