Welcome to the SoyBase Affymetrix GeneChipV1 Genome Viewer Page
This page is designed to report sites in the soybean genomic sequence that have Affymetrix&trade GeneChip® Soybean Genome Array probe set matches. All of the locations for each probe set (which comprise 8-11 25 base probes)
were identified on the Willimas 82 genome sequence using BLAST. Probes were considered a match to the genomic sequence when the sequence identity was at least 24 of the 25 bases.
To search for matches to a probe set, upload a text file of a list of the probe sets you are interested in. The search will return a table that contains the list of genomic locations which have sequences matching at least one
of the 25 mers that make up the probe complement for each probe set (see here for an example of the returned table). For reference,
probe set names will be similar to Gma.10029.1.S1_at or GmaAffx.23664.1.S1_at.
We have found that the most reliable way to submit a list of probe set names is to copy the names from a spreadsheet or other report and make a new text file with the list. The format of the file should have a single Affymeterix
probe set name per line and the file should be saved as ASCII text.
Enter the name of a text file containing a list of Affymetrix probe set names here:
Paste a list of Probeset names here (one name per line)
Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA