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. 2011 May 23;39(Web Server issue):W107–W111. doi: 10.1093/nar/gkr248

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© The Author(s) 2011. Published by Oxford University Press.

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.

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Figure 2. — The PET(co)fold output for the antisense RNA FinP regulation of the 5′-UTR of the major F-plasmid transcriptional activator TraJ based on the sequence alignment without paralogs from Rfam 10.0: (a) the dotplot of FinP with base pair reliabilities in upper left triangle and MEA-structure in lower right triangle produced by PETfold; (b) the dotplot of TraJ produced by PETfold; (c) the concatenated Rfam seed alignments with sequence conservation indicated, the PETcofold predicted structure in dot-bracket format and base paired reliabilities; (d) the PETcofold predicted RNA binding structure. (a) and (b) show the output produced by the PETfold web server and (c) and (d) show the output produced by the PETcofold web server. Intra-molecular pairing is denoted by round brackets in (c) and arcs in (d) and inter-molecular pairing is denoted by curly brackets in (c) and straight lines between both sequences in (d).