Introduction
For the release of IGB 6.5, we have created a Sequence Viewer. This pop-up window will allow a clean view of the sequence that a user selects; when the genomic sequence of a gene model is chose, the exons and introns are shown in different colors, but the viewer can also be set to show cDNA from the model. Start and stop codons are shown, when the information is available, and the viewer allows all possible translations. The data can be copied into a text file or exported as a fatsa file, making this viewer a helpful and convenient tool for examining either a gene model or a user-defined area of sequence.
The first step is to ensure the sequence is loaded (Data Access tab > Load All Sequence button OR > Load Sequence in View button).
Viewing a Gene Model/ Annotation
For gene models/ annotations, simply right click on the annotation. You can chose an individual exon to view, or you can Select Parent and then right click again to view the whole gene model; chose Show genomic sequence. 
This will immediately open the Sequence Viewer (see picture below). In the Viewer, exons will be shown in yellow and introns will be shown in white. If a single exon was chosen, it will appear in yellow. The start codon (ATG) is shown with a green box around it, and the stop codon has a red box around it. 
If this color scheme is difficult for a user, the Change color scheme button will invert the black and white, and change the yellow to blue. 
The title of the viewer window will indicate what gene model/ element it is showing. In our example, this data is the A_thaliana_Jun_2009 genome version, and specifically the TAIR10 mRNA. The gene we are looking at is on chromosome 1, it's ID is AT1G07350.1 and it is on the minus strand.
Changing the View
The Sequence Viewer has several options to change the view. When looking at a whole gene model, the viewer will allow you to select Show cDNA only, which will eliminate exons from the shown sequence. We recommend selecting this option before using the translation feature.