Some of the feature appearance options that are available. Each feature's shape, visibility, color and panel position is configurable. The result panel can display the complete portfolio of computational results. The top three rows of this figure use small vertical green lines to indicate the position of start codons in the genomic sequence in all three possible translation frames. The second set of three rows does the same for stop codons (red). This enables curators to easily discern ORFs. Beneath this, in orange, are BLASTX hits to other species. Every row represents a separate alignment in this expanded view (see Figure 3 for a discussion of the expanded view). In each alignment the high-scoring pairs (HSP) are separated by two parallel lines to indicate alignment gaps. Seeing what features share edges is important during annotation for adjusting exon-intron boundaries. When an item is selected, corresponding edges of other items that end at the same nucleotide are highlighted with a white line (arrow A). The small turquoise triangle indicates the site of a P-element insertion. The rows of light green rectangles are Sim4 alignments of Drosophila ESTs to the genome. When a 5' and a 3' EST are derived from the same cDNA clone we connect them with a dashed line (arrow B). This contrasts with the solid lines used to represent the gaps, corresponding to introns, introduced into an EST to permit its alignment to the genome. The final piece of computational evidence shown in this figure is the gene prediction, shown in lavender. In this example, we have intentionally represented introns in two different ways - as straight or peaked lines - as an illustration of Apollo's configurable graphics. In the annotation panel, the curator has created two alternative transcripts for this gene, each of which is supported by multiple pieces of EST evidence. Individual exons that the curator has selected are outlined in yellow. The translation start and stop sites are shown as green and red vertical lines, respectively. Each individual curator has a signature color; any annotation that this particular curator creates is shown in bright blue. In the sequence panel the scale is drawn in red to indicate that this gene is on the reverse strand.
Lewis et al. Genome Biology 2002 3:research0082.1-0082.14 doi:10.1186/gb-2002-3-12-research0082