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 changing axis appearance are here. You can change the foreground and background colors or customize the format used to present numbers. Changes to the colors take effect after closing the Preferences window.

You can alter how the numbers appear as follows. 

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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. ABBREV will show the numbers as abbreviated as is reasonable, with unit designations. For example, when zoomed out, numbers appear as 10M, 20M etc. Changes made here to Number Format take effect immediately. 

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ORF (Open Reading Frames) Analyzer

These preferences affect colors used to indicate stop codons and the ORFs 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

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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. Changes made in this section will be applied to the image after the Preferences window is closed.

Tip: Reset residue colors to whatever the Axis backround color to avoid coloring bases. showing your current  colors to the current background color of the If you do NOT wish for individual residue highlights, set the colors to white. 

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Click a color swatch to change base colors.

ORF (Open Reading Frame) Analyzer

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.

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, and before you load very large files, >100MB. Each of these warnings has the option Do to not show be shown again. If you decide that you do want the warnings to appear, you can reset your choice from this pane. Check (or uncheck) Ask before exiting, Confirm before delete and/or Confirm before load.

Sometimes, the zoom stripe obscures sequence that you are interested in, or is otherwise distracting. You can hide the zoom stripe entirely by unchecking Keep zoom stripe in view.

If many changes have been made throughout the IGB interface, and you would like to start over (new user for instance) or if IGB is behaving 'oddly', you can Reset all preferences to defaults. Be careful, as this WILL reset ALL preferences by deleting the preferences file. You cannot undo this function!

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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.