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BioMed Research International
Volume 2013, Article ID 984028, 15 pages
Research Article

A Genome-Wide Analysis of RNA Pseudoknots That Stimulate Efficient −1 Ribosomal Frameshifting or Readthrough in Animal Viruses

1Department of Computer Science, Southern Illinois University Carbondale, IL 62901, USA
2Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, IL 62901, USA

Received 8 April 2013; Accepted 21 August 2013

Academic Editor: Marcelo A. Soares

Copyright © 2013 Xiaolan Huang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

In a computer-generated output (figure below), the sequence elements of the detected pseudoknot (See Figure 1 of the article for sequence elements of a pseudoknot) and a sequence of 20 nt preceding the pseudoknot are shown in three lines. The first line is for L2 and L1. The second line is for S1-3’ and S2-5’ sequences. The third line is for the 20 nt preceding sequence (which may contain the slippery sequence and spacer region), S1-5’, and S2-3’ sequences. Note that the 5’→3’ orientation of the sequence in the second line runs from the right to the left, which is opposite to the sequences in the other two lines. The free energy (∆Go37) values for the two stems S1 and S2 are calculated and indicated. The output also indicates the starting/ending positions of the pseudoknot-forming sequence, the number of nucleotides in the stems/loops (S1, S2, L1, L2, and L3) of the pseudoknot. The detected pseudoknots in a viral genome are ranked by the calculated free energy values.

In the sample output, some pseudoknots have their pseudoknot-forming sequences overlapped (such as the first and second ranked pseudoknots), meaning that the pseudoknots cannot exist simultaneously. The overlapped pseudoknots with a higher free energy are indicated by a line through the middle of the selected text.

  1. Supplementary Material