MutualFold is an application to next-generation sequencing based RNA structure probing.
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J Comput Biol. 2014 Aug;21(8):609-21. doi: 10.1089/cmb.2013.0044. Epub 2014 Apr 1.
Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing.
Zhong C1, Zhang S.