<p>Figures for ‘Visualizing and exploring genomic information for non- protein-coding RNA identification using ApolloRNA’</p><p>Figure 1</p><p>(a) An ‘Environment Variables’ window displaying both user and system defined variables on Windows operating system.</p><p>(b) A ‘New User Variable’ window allowing to define a user variable (name and value) on Windows operating system.</p><p>1 (c) An Apollo load data window that allows to specify the format of input data and the file to load.</p><p>(d) An Apollo main window that displays both GenBank annotations (in the blue parts) and TransTermHP data (in the black parts) of the Pyrococcus abyssi GE5 genome. The inorganic polyphosphate/ATP-NAD kinase protein annotation is selected (surrounded in red). So the information associated to this annotation is displayed in the lower part of the window.</p><p>2 Figure 2</p><p>(a) An ApolloRNA window that displays the predicted secondary structure of the current selected sequence: tRNA-Ala. </p><p>(b) A portion of an Apollo main window showing the selection (surrounded by a red line) of a subsequence from 1403702 to 1403711 in the direct strand using the middle mouse button to surround the corresponding nucleotides.</p><p>3 (c) An ApolloRNA window to parameterize and launch RNA/RNA interactions search for the currently selected sequence. </p><p>4</p><p>(d) An ApolloRNA window that lists predicted RNA/RNA interactions for the currently selected sequence</p><p>(e) An ApolloRNA window that displays a predicted interaction between two sequences. The currently selected sequence is written in blue and the predicted target in red.</p><p>5 Figure 3</p><p>(a) An ApolloRNA window to configure the display of quantitative variables. </p><p>(b) A Apollo main window displaying two additional graphs: in blue, the GC% computed on a 101 nucleotides sliding window graph and in red, the minimum free energy computed on a 150 nucleotides sliding window. In the bottom of the window, some information are displayed on the selected 16S ribosomal RNA of the Pyrococcus abyssi GE5 genome.</p><p>6</p>