Figure 5.1: Screenshot of the main window of 
.
The organisation of the main output of the gui is depicted in fig:qod:main. It displays graphically the segmentation in mcis (diagram 1), plots the number of mcis covering each base pair (diagram 2). It also describes textually all mcis (left text subwindow), and the fragments of the partition (right text subwindow).
In both diagrams, the x-axis is the genome position. In diagram 1, the thick, black bar represents the central genome, while color bars above and below it represent the mci. The mci position above or below is unrelated to the strand on which similarity was detected. mci are drawn in lines such that all mci on a line share the same color and two overlapping mci are displayed on different lines. In the mci text window, mci keep the same color as in the diagram. In diagram 2, the y-axis gives the number of mci covering a position. For a line at level 1, only a single alignment may be available for the unique mci. In which case, this absence of ambiguity for homology is displayed by a green coloured line. When the line reaches level 0, meaning the absence of similarity, it is colored in red. Again, this color scheme is respected in the segmentation description (left text section). At any time, the interval corresponding to the current selection (mci or feature) appears as a thick black line on the y-axis of the second diagram.
As mentionned previously (see Annotation Transfer), if genome
pairwise similarity alignments are provided (see --axt
option, Invoking qod and qodgui) as well as the annotations of
the central genome, qod and
extracts from the
segment possible alignments the sub-alignments corresponding to
annotated features and displays them on the gui.
All features located in uniquely aligned segments are marked as transferable from the center to any other compared genome. The user can then select according to a minimal percent of identity or from a feature list, which annotations he wants to transfer, and export the list in various formats (Genbank/Embl/Sequin, see fig:qod:transfer).
