Introduction

The Sliced View tab displays an alternative view of items selected in the Main View. It is especially useful with displays the same data as in the Main View but deletes some of the intronic "space" within gene models.

It is mainly useful in depicting mammalian genes which can span vast regions of genomic sequence but which are comprised mostly often span many kilobases and mostly consist of intronic sequence. The Sliced View aims to give you a higher level summary of gene structures by condensing the intronic regions and allowing you to focus on the exons, relative to each other. For details about using this feature, see Track appearance.

The following image shows how this works. The top panel of the IGB Main View window shows the normal, non-spliced view of a region containing overlapping genes from a human, AGBL4 which contains several very large introns, one of which completely encompasses another gene, BEND5.  The Sliced View panel on the bottom shows AGBL4, and then BEND5, but with the intronic sequences reduced to 100bp.  The points where the introns were shortened appear as black hash marks in the coordinate axis of the Sliced View tab. Note how the Sliced View makes it easy to see the gene structures, whereas in the main view the exons of AGBL4 are so small it is impossible to even see size comparisons of the exons it contains.

You can enter the size you want the introns to be set to by changing the number in the Slice Buffer (default is 100). By unchecking the Slice by Selection box, you can move the Main View to another region of interest, and click on other features without changing the Sliced View.

Another feature that the Sliced View panel supports is finding open reading frames (ORFs) and stop codons. For details on using this function, please see Track appearance.