Additional file 10.
Analysis of potential duplexes formed by predicted intergenic ncRNA transcripts. First, we filtered potential duplexes by fast searches for overlap regions with wublast (Gish, W., personal communication) with parameters that also allow for G-U basepairs, as described in Steigele et al . Second, the thermodynamically preferred duplex between two predicted RNA molecules was calculated by RNAcofold. In most cases, only very large overlaps between predicted RNA molecules were found.
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Steigele et al. BMC Biology 2007 5:25 doi:10.1186/1741-7007-5-25