Bio::POD offers several levels of navigation and incorporates multiple sources of data to improve the viewing and understanding of a gene:
The top pane of the application is the Transcript View which displays the gene in mature RNA form (exons only, including UTR). This pane is highlighted in the image below:
The blue segmented bar along the bottom is the gene. Each rounded square represents an exon. The start codon is highlighted in green and the stop codon is highlighted in red.
The annotation displayed above the gene and the PAR graph at the top of the Transcript View panel are specific to the mature RNA displayed in this pane. For more on annotation and the PAR graph, view Understanding Annotation and Prioritized Screening.
The middle pane is the Genomic View which displays the entire gene (exons and introns) plus flanking 3' and 5' sequence. This pane is highlighted in the image below:
Again, the blue segmented bar at the bottom is the gene. This time, the thinner bars are flanking sequence and introns, the thicker bars are the exons. The images above the gene represent annotation and the graph at the top of this pane is the genomic PAR graph for the gene.
The bottom pane in Bio::POD is the Navigation View. Similar to the Genomic View, the Navigation View displays the entire gene plus flanking sequence. However, the gene is not drawn to scale in this view. It's primary purpose is to act like a "You Are Here" sign on a map. The portion of the gene that you are currently viewing in the above panels are highlighted in the Navigation panel. In the case of this image:
...the entire gene is in view so each exon is highlighted in blue. However, when you zoom in as described in the next section, only a subset of the exons are highlighted to show you where you are in the gene. See the next section on zooming for an example.
This unique feature allows you to see the entire gene at once in a "bird's eye" view or up close on a nucleotide-by-nucleotide level. By default, the zoom level is zoomed all the way out, allowing you to see the entire gene including exon/intron splicing and annotation.
By clicking the "+" button in the center of the application, you begin to zoom in on a smaller and smaller portion of the gene to the point where you can see the nucleotides and amino acids of the gene as shown here:
Notice in the Navigation View on the bottom that only the first two exons are highlighted in blue. This indicates that you are zoomed in to the first two exons of the gene.
Gathered annotation about the gene is displayed in both the transcript and genomic views in the areas above the gene as pictured below. The annotation in the Transcript View window is coding specific such as functional domains and secondary structures. The annotation in the Genomic View window is everything else (not specific to the coding portion of the gene) such as SNPs.
For more on annotation, view the documentation on Understanding Annotation and Custom Annotation.
Once you understand the basics of navigating a gene in Bio::POD, you may be interested in better understanding the PAR algorithm. Information can be found in the Prioritized Screening documentation.