Figure 2.

A typical output of running the PKscan program, using the full-length genomic mRNA of the simain retroviruses type-1 (SRV-1, accession number M11841) as the input sequence. A total of 50 pseudoknots with a calculated stem free energy lower than- 18 kcal/mol were identified (only the 1^st & 2^nd ranked pseudoknots are shown for clarity). The texts and boxes in red are not parts of the original output. They are added to indicate the sequence elements of the identified pseudoknots. The software can be downloaded from: http://www2.cs.siu.edu /~xhuang.