This tab contains several options addressing the color/appearance of non-track elements in the image, as well as some other miscellaneous options.

Axis

The options for axis appearance are here. You can change the foreground and background colors to suit your needs. Changes to the colors will not appear dynamically, but will take place when the Preferences window is closed.

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Introduction

Select File > Preferences > Other Options to configure the following:

• Coordinates track number format
• Sequence base colors
• ORF analyzer
• Edge matching
• Gene model translations
• Track resizing
• IGB exit and data set loading behaviors

Preferences Other options
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Coordinates

These are options for changing number appearance. FULL shows the number with no thousands separators and the unit 'kb'. COMMA shows the numbers with commas at every 10^3 (American U.S. style) and with no unit designations. This is the default appearance. ABBREV will show the numbers as abbreviated as is reasonable, with unit designations, i.e. zoomed all the way . For example, when zoomed out, numbers are appear as 10M, 20M etc. Zoomed in a bit, numbers are shown as 19,500k, 20,500k. Zoomed all the way in, numbers are shown fully. Changes made here appear dynamically in your image.
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Residue Colors

IGB displays letters representing DNA bases (residues) when zoomed-in. Residues are shown in alignment tracks, sequence tracks, and in underneath the coordinate axis.

By default, IGB uses cool colors for A and T residues and warmer colors for G and C residues. Other refers to residues that are either 'N', 'X' or '-' (missing) and can be set to a bright color if you are looking for deletions in short read sequences; otherwise you may wish to leave it as the neutral gray.

Click a color swatch to change base colors.

ORF (Open Reading

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Frame) Analyzer

This set of preferences changes the color of the stop codons and the ORFs These preferences affect colors used to indicate stop codons, the ORFs and the background of the ORF tracks that are shown in the Sliced View tab. After setting new color options, uncheck and recheck the Analyze ORFs option in the Sliced View tab to show the new color scheme.
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Change Residue Colors

IGB shows each residue with an individual color highlight at the fully zoomed in level. At less zoom, where the letter cannot be fully shown, IGB will still show the color for each residue. Zoomed out to the point where IGB cannot resolve individual bases, the sequence will appear as a gray bar. In this section, you can change what color represents each residue individually. If you do NOT wish for individual residue highlights, set the colors to white. Changes made in this section will be applied to the imageafter the Preferences window is closed.
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Edge Match

Edge matching highlights features that have identical boundaries. Edge matching becomes active when you click items in the display.

Click the swatch to change the edge match color. The selected color applies all annotation tracks.

Codon Display

The Codon Display is activated when the sequence of a gene model is loaded and the user zooms in close enough to see the sequence. The codon translation appears within the gene model. User can set the amino acids to appear in one letter format (default), three letter format or be hidden. The colors is based on the chosen foreground color for the track.

Track Resize Behavior

Track Resize Behavior is how IGB adjusts other tracks when a specific track height is changed. Adjust All Tracks means that as a single track is increased in height, all other tracks are reduced by a commensurate amount. Adjust Adjacent Tracks (default) means that all added or subtracted height is removed/added to the bordering track, leaving the rest of the display unaffected.

Data loading and exit behaviors

Confirmations

IGB warns you when you are about to exit the program and before you delete a file or files. Each of these warnings has the option to not be shown again. To turn off these warnings or reset your previous choice, check (or uncheck) these options.

Reset all preferences to defaults

Click Reset preferences to defaults to reset all the preferences to the IGB defaults. This is sometimes useful if you need to troubleshoot IGB.