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. 2011 Aug 31;2:54. doi: 10.3389/fgene.2011.00054

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Copyright © 2011 Okada, Saito, Sato and Sakakibara.

This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and other Frontiers conditions are complied with.

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An example of the results on CLUSTL W alignments with low entropy. Predicted common secondary structures of five sequences in HIV_PBS family are shown. (A) The common secondary structure predicted by CentroidAlifold with γ_a = 1.0. (B) The common secondary structure predicted by RNAalifold. (C) The common secondary structure predicted by CentroidAlifold with γ_a = 1.0 for one of the negative control alignments generated by SISSIz. (D) The common secondary structure predicted by RNAalifold for one of the negative control alignments.