IGB offers several tools to highlight patterns to aid in making comparisons. These are described in the following sections.
Highlighting matching endpoints
To see if different data sources show the same start and endpoints for an annotation:
- Select an item.
Matching edges of corresponding items in all tracks being viewed will be highlighted
- By default, the highlight color is white, which works well on a black background. If you change the background color, you may want to change the edge-matching color as well.
Use View menu > Adjust edge match fuzziness > Edge Sensitivity Adjuster dialog box > Edge match colors > Standard.
To specify the degree of closeness required for a match (how many base pairs difference is still considered a match):
- Choose View menu > Adjust edge match fuzziness.
- Slide the slider to the maximum number of base pairs difference that you want to consider a match.
By default, if edge match fuzziness is adjusted, all matching edges are highlighted in gray rather than in white. This color can also be changed using View menu > Adjust edge match fuzziness > Edge Sensitivity Adjuster dialog box > Edge match colors > Fuzzy matching.
Slicing
Slicing makes slight variations more visible when comparing multiple annotations on the same sequence. Slicing cuts out long introns and realigns the exons of a selected annotation or set of annotations, making pattern irregularities and possible alternate splicing more obvious.
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To compare multiple selections:
- In the main view, select all annotations to include in the slice. In the example above, you would select all 6 "copies" of the gene.
- Click the Sliced View tab.
- If desired, resize the tab panel or window to enlarge the viewing area of the Sliced View window.
- Make sure the Slice By Selection checkbox is checked.
IGB may take a few moments to display the sliced region. For easy comparison, the sliced view displays sliced versions of all annotation tracks and graphs in the region being viewed.
Use the zoom and scroll bars to navigate in the sliced view panel. Note that the numbers in the Coordinates track in the sliced view panel indicate scale; they don't correspond to genomic coordinates. Endpoint matching in the upper and lower windows are independent of each other.
Note: If you use keyboard shortcuts for zooming and scrolling, the shortcuts will apply to both the main view and in the sliced view. The effect can be confusing when both views are visible in the same window at the same time. Opening the sliced view in a separate window can give more predictable shortcut behavior. See Opening tab panels in new windows .
Viewing deletions and insertions
When several transcripts share the same or overlapping exon regions, the slice view can help you to see where exons were deleted in one transcript relative to another one.
To examine alternate splicing, select only one of the transcripts in the main view. The slice view will show all transcripts as they have been sliced relative to that selected transcript.
In this image, the top-most transcript was selected in the main view. The other three transcripts each include one or more exons that are not included in the top transcript. The locations of these sliced-out (deleted) exons relative to the other exons is indicated with small "X" marks. 
Disabling the sliced view
Slicing requires extra computation. Although this computation occurs on a background thread, you may still wish to turn it off to increase the speed of other computations.
You may also want to turn slicing off so you can preserve a static view of a particular result.
Turn slicing on and off with the check box Slice by Selection in the Sliced View tab panel.
Adjusting the sliced view
Each sliced region includes a buffer, in order to allow examination of the bases in the intron-exon boundary. The buffer is initially 100 bases on each side of each sliced region; if an exon in the same range that was not selected for slicing extends beyond the buffer, it may be truncated. To avoid this problem, increase the buffer enough to accommodate the entire exon by changing the number of base pairs before and after each exon.
To adjust the buffering number of base pairs before and after each exon:
- Visually estimate the number of base pairs required to achieve the adjustment needed
- In the Sliced View tab, change the value in the Slice Buffer field.
- Press the <Enter> key.
You may also set the slice buffer to 0 to completely eliminate the introns. This can be useful in conjunction with the Analyze ORFs function to find open reading frames. See Showing ORFs and stop codons.