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Probe set alignments - link.psl files
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.
About probe set alignment visualizations
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 individual probes from regions near the 3' end of the expressed sequence. Affymetrix (as of 2014) distributes probe and target sequences on their Web site, where "target sequences" contain the 3' end regions from which the probes were selected.
If you have questions about what you see in a probe set alignment, let us know.
Why this is useful
Often multiple, seemingly redundant probe sets interrogate one gene. This situation mainly arises when a gene has multiple, alternative three-prime ends due to alternative splicing or alternative termination sites. If an experiment identifies genes where redundant probe sets are differentially expressed with different fold-changes or in opposite directions, this can indicate that the treatment affects splicing as well as the overall abundance of RNAs arising from the gene.
Thus if you observe redundant probe sets that give different or contradictory results, it's a good idea to view them in IGB and compare their alignment to annotated genes and transcripts.