Table 3.

GATAPlotter windows and features

Tools Window
Score Sliders	Sliders can be used to control the minimum score and maximum score used in deciding which sub-alignment box-line-boxes are displayed. The units are a normalized range where zero is set to the value assigned in GATAligner to the Lower Score Cut Off. 100 is set to the value obtained by multiplying the Window Size by the Nucleotide Match. The actual window bit and Expect values set by the sliders are shown in the adjacent boxes. Since the shading is relative to these minimum and maximum values, be careful in making comparisons in shading between two GATA plots. Such comparisons are only valid if the same window size, cut off score, and scoring scheme were used. Check the actual score by clicking on the shaded box or connecting line to see the real bit score. (Bit scores are scoring system independent and can be used to directly compare alignments. Raw scores are relative to the settings for match, mismatch, gap, etc.)
Zoom Buttons	The zoom buttons allow for zooming in and out.
Ref or Cmp	These numbers report the position of the mouse, in base pairs, when the mouse passes over one of the sequence bars.
Mouse Clicks	Single clicking a gene annotation feature retrieves and displays all information associated with that feature in the Text Console Window. Likewise single clicking an alignment box or line displays the sub-alignment information. Double clicking fetches the sub-alignment and its parental local alignment. The sub-alignment is indicated by the asterisks in the larger local alignment. All visible alignments beneath a mouse click are retrieved. Use the Score Sliders to determine which boxes are visible.
	If you are interested in a sub section of the alignment, drag the mouse over the region and a reformat box will appear. If you drag the mouse over one sequence and it contains box-line-boxes, these will to used to fetch the corresponding sequence from the other sequence. If you drag the mouse over both sequences, sub sequence sections will be retrieve regardless of the location of box-line-boxes.
Text Console	A resizable scrolling container for text messages generated by mouse clicking.