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. 2009 Jun 3;3:51–69. doi: 10.4137/bbi.s2578

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Copyright © 2009 The authors.

This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/2.0/).

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Figure 7. — Consensus structures generated from the roX2 RNA sequence alignment. A) The consensus structure produced by RSpredict. B) The consensus structure predicted by KNetFold. C) The consensus structure predicted by Pfold. D) The consensus structure predicted by RNAalifold. RSpredict, KNetFold and RNAalifold, all with MCC = 1, performed better than Pfold with MCC value of 0.88. Note that each gap in the consensus structure in (a) represents a column with more than 75% gaps in the roX2 RNA sequence alignment. All the columns with more than 75% gaps are deleted to obtain the refined alignment based on which RSpredict generates the consensus structure.