Introduction

The Sliced View tab displays an alternative view of items from in the Main View. In 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)

Using Sliced View

• Click the Slicked View tab to make it the active bottom tab
• 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 appears in the Sliced View but intronic regions are removed

Sliced View options

The bottom row of the Sliced View panel shows options for controlling Sliced View appearance.

Sliced View options (click to enlarge)

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" consists of intronic sequence on the five and three prime ends of exons.

Analyze ORFs

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

Min ORF Length

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 alternative splicing.

To examine alternate splicing using the Sliced View

• select one or more transcripts in the Main View
• deletion icons (X characters) IGB draws on the other transcripts
• insertions are shown as larger introns

Insertion example

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.

Deletion example

In the next image, the bottom-most transcript was selected in the main view. The other three transcripts each include one or more exons that were present in the top transcript. The locations of these "sliced-out: (deleted) exons relative to the other exons is indicated with X marks (red boxes). The exons that are 'shorter' than the matching exon in the selected track are drawn shorter (blue box).

Showing ORFs and stop codons

The Sliced View panel can show open reading frames and stop codons.

To visualize open reading frames and stop codones

• select an annotation in the Main View
• click the Sliced View tab
• check the Analyze ORFs checkbox
• use the Min ORF slider to adjust the mininum length of ORFs to show (in base pairs)

Three rows of ORFs appear for + translations (blue box), and for each - translation (purple box). Stop codons are red hash marks, and the reading frames are marked as green lines. The color of the stops, the ORFS and the background can be changed using Preferences > Other Options (see Other Options).