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. 2015 Mar 16;12(2):197–207. doi: 10.1080/15476286.2015.1017206

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© 2015 The Author(s). Published with license by Taylor & Francis Group, LLC

© Jan Reinkensmeier and Robert Giegerich

This is an Open Access article distributed under the terms of the Creative Commons Attribution-Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The moral rights of the named author(s) have been asserted.

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Figure 4. — Pipeline for cuckoo RNA discovery based on TDMs. Different colors correspond to structural variants of cuckoo RNAs (HP2 in blue, HP3 in green, HP4 in red). Bacterial genome sequences from the NCBI reference genome database were gathered and consecutively scanned by the skeleton TDM, focusing on primary sequence conservation, and the cuckoo TDM, which incorporates structural constraints. Then the energy filter is applied. HP2 cuckoo candidates that pass the structural filter are processed by the HP2 cuckoo TDM which was adapted to match specifically HP2 cuckoo RNAs.