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. 2022 May 3;23:159. doi: 10.1186/s12859-022-04673-3

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 3 — Creating the guide structure in KnotAli. Five sequences are shown from the full alignment of tRNA sequences. Arcs between columns of the alignment represent the $MIp$ values for the two columns at the two ends of the arcs. Arcs extending the same column represent change of $MIp$ with a shared column. Here, we only represent a subset of the $MIp$ values. The bottom line represents the determined guide structure for the alignment. As shown in the guide structure, only non-conflicting base pairs with high adjusted mutual information are selected as the intermediary base pairs, and later included in the guide structure