Figures for ‘Visualizing and exploring genomic information for nonprotein-coding RNA identification using ApolloRNA’
Figure 1
(a) An ‘Environment Variables’ window displaying both user and system defined
variables on Windows operating system.
(b) A ‘New User Variable’ window allowing to define a user variable (name and
value) on Windows operating system.
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(c) An Apollo load data window that allows to specify the format of input data and
the file to load.
(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.
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Figure 2
(a) An ApolloRNA window that displays the predicted secondary structure of the
current selected sequence: tRNA-Ala.
(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.
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(c) An ApolloRNA window to parameterize and launch RNA/RNA interactions
search for the currently selected sequence.
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(d) An ApolloRNA window that lists predicted RNA/RNA interactions for the
currently selected sequence
(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.
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Figure 3
(a) An ApolloRNA window to configure the display of quantitative variables.
(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.
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