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IGB can be used to visualize data from Affymetrix showing the locations of GeneChip Expression Array probe sets and target sequences aligned to a genome.

In most Affymetrix arrays, probes are grouped conceptually into probe sets, groups of probes that are expected to measure expression for individual known or computationally-deduced mRNA molecules. 

These target sequences may be identical to known mRNA sequences in GenBank, or they may have been produced computationally by merging ESTs or mRNA sequences into a single sequence, sometimes called a "consensus" sequence.

IGB can display location of design sequences and probes within the genomic sequence. Probe set alignments are available as "link.psl" files from the Affymetrix Web site. Some probe set alignments are also available from Affymetrix and IGBQuickLoad data sources in the Available Data sub-panel of the Data Access planel.

Viewing probe sets from IGB DAS

To view probe sets available from IGB DAS2 data source

  • Open the Data Access panel
  • Open the IGB DAS / affy folder under the Data Sources and Data Sets section of the Data Access tab.
  • Click the checkbox next to the array you would like to examine
  • zoom to a gene or region of interest and click Load Data.

The probe set, including the target sequence and individual probe, will appear in IGB.

Where to find probe set alignment files

Many are available from the Affymetrix customer support Web site.

To obtain these files, go to the Affymetrx site and look for the array you are interested in.

On the array's support page, look for alignment data files in the "NetAffx Annotation Files" section. Look for files labeled as consensus alignment files or something similar. Note that alignment data files may not be available be available for species with well-characterized genomes.

Affymetrix distributes these files in an Affymetrix-specific format called "link.psl" which IGB can read.

These files consist of two sections:

  • Alignments of the target sequences onto the reference genome (ordinary PSL format)
  • Alignments of probe sequence onto the targets
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