Table 2

GATAPlotter menus

File-Menu

Open or Close Alignments

Open a new GATA plot or close the present GATA plot.

Quit

Quit the entire application.

Save GATAPlot Image

Use to save a high resolution PNG file of the GATAPlot.

Save GATAPlotter Settings

Select this menu option to save the current settings. These will be used upon opening new GATA plots. Generic Track settings are not saved. To restore the defaults, select the Redraw Using Defaults from the Windows menu and then the Save GATAPlotter settings. Alternatively, delete the GATAPlotterPreferences file in the GATA folder.

Alignment-Menu

Sizing parameters

A variety of parameters to change the height, width, thickness and relative location of the Alignment panel shapes.

Set Nucleotides Per Pixel

Allows for specifying the number of nucleotides that are rendered per pixel enabling size synchronization between different GATAPlots.

Fetch Conserved Sequences

Use this option to reformat both the reference and conserved sequence using the visible alignment boxes in the GATA plot. Upon selection, a dialog box will appear asking how you would like to reformat the non-boxed sequences. These non-conserved sequences can be replaced with any single character (e.g. N or X) or converted to lower or upper case. Use the sliders in the Tools Panel to adjust what is visible.

GATAligner Parameters

Select to retrieve all the GATAligner settings used in making the GATA alignments and GATA plot. (e.g. score cut off, window size, match, mismatch, etc).

Annotation-Menu

(These menu items are only available if gene annotation has been added to the GATA plot.)

Gene Groups

Use to hide or show all of the gene groups (Protein, RNA, DNA) or labels.

Protein, RNA, DNA

Select whether to hide, show or change their colour.

Scale Ruler

Select to hide or show, change the colour, or move the scale bar.

Tracks

This option contains global effectors for generic tracks.

RefTrks/ CompTrks

If generic features are found within the GFF file, each is assigned its own track. Their thickness, colour, visibility, and label visibility can be modified using the appropriate options.

Pix Btw

A variety of adjustments can be made to the number of pixels that are placed between features. Negative numbers are valid if you want to overlap features.

Line Thickness

Line thickness can be set to control the size of Protein, RNA, and DNA features.

Colour

The background panel and label colour can be set using these options.

Scale Track Colours By Score

If generic tracks have been generated and are associated with a score, they can be shaded using the scaling feature. Select the method GATA should us to convert the reported scores to linear numbers. (e.g. Often hits to a position weight matrix are scored in log units. Select the appropriate base log 10, log 2, or natural log.) After converting the scores for a particular track, a range is estimated and used to adjust the opacity of each feature from 30% for the lowest scoring feature to 100% for the highest scoring feature. This allows visual comparison of features within a track. Comparisons between tracks are only valid if they have the same range.

Windows-Menu

Show All

Retrieves and displays all hidden windows.

Hide All

Hides all windows except the main GATAPlotter alignment window.

ReDraw Using Defaults

Redraws all panels using GATAPlotter default values.

Documentation-Menu

Extensive documentation for GATA including examples.


Nix and Eisen BMC Bioinformatics 2005 6:9   doi:10.1186/1471-2105-6-9

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