IGB can display Affymetrix probe sets aligned onto a reference genome - it can show probe set design sequences aligned onto a genome with the locations of the probes indicated as blocks.
You can also make your own probe set alignment files using blat, tabix, and a python script we wrote. For more information, see this Bitbucket repository.
Depending on when the arrays were designed, Affymetrix typically used expressed sequences from GenBank to select probes for probe sets - these expressed sequences were sometimes called "exemplar" or "consensus" sequences. They then selected a region individual probes from regions near the 3' end of each and then selected individual probes from that region. They distribute the sequences of probes in a probe set the expressed sequence. Affymetrix (as of 2014) distributes probe and target sequences on their Web site, along with files labeled where "target sequences" that contain the region 3' end regions from which the probes were selected. They also distribute what they call "exemplar" and "consensus" sequences taht contain the smaller target region from which the probes were selected.
Probe set visualization visualizations in IGB show the alignments of target, exemplar, or consensus sequences onto the genome. They also show the locations of probes that were selected from the design sequence. See the preceding figure for an example.
If you have questions about what you see in a probe set alignment, let us know.
Why this is useful
Often a gene