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The Sliced View tab displays an alternative "sliced" view of items selected from in the Main View. It displays the same data as in the Main View but compresses genes models by trimming intronsIn the Sliced View, introns are shown as having the same size, set in the Slice Buffer box). The Sliced View also can show open reading frames (ORFs).

Sliced view example (click to enlarge)

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• Click the Slicked View tab to make it the active bottom tab
• For maximum usefulness, open Open the Sliced View tab in a separate window (this is optional) Tabs > Open Current Bottom Tab in New Window)
• Click a gene model in the Main View
• Observe that the same gene model shown appears in the Sliced View but with compressed intronic regions
• Note that the Coordinates track in the Sliced view are relative to the start of the Sliced View region; they don't indicate absolute genomic coordinates.

Sliced View options

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Sliced View options

Slice by Selection

This option controls when the Sliced View updates. Check this option to ensure that whatever is selected in the Main View is shown in the Sliced View display.

Slice Buffer

The Slice Buffer setting controls the size of introns drawn in the Sliced View display. The "buffer" is sequence flanking exons.

Analyze ORFs

Check this option to activate display of ORFs (open reading frames) underneath the Sliced View coordinate axis * track.

Min ORF Length

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.This option controls the size of ORFs shown when Analyze ORFs is checked.

Viewing deletions and insertions

The Sliced View can help you see where sequences present in one transcript are absent from the others due to alterantive alternative splicing.

To examine alternate splicing using the Sliced View

• select one of the transcripts in the Main View
• observe insertion icons (X characters) IGB draws on the other transcripts

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In the first image, the arrows show how IGB draws regions where an annotation is 'inserted'; the introns in 'non-inserted' tracks are elongated over the region of insertion.

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