PCSHMM (Profile-csHMM, Profile Context-Sensitive HMM) is a software for finding structural alignment of RNAs including pseudoknots based on profile-csHMMs
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Structural alignment of RNAs using profile-csHMMs and its application to RNA homology search: Overview and new results
Byung-Jun Yoon and P. P. Vaidyanathan,
IEEE Transactions on Circuits and Systems: Part-I, IEEE Transactions on Automatic Control (Joint Special Issue on Systems Biology), vol. 53, pp. 10-25, Jan. 2008.