[Arabidopsis] seeking TAIR9 bpmap file for Arabidopsis tiling array 1.0R

Ann Loraine via arab-gen%40net.bio.net (by aloraine from gmail.com)
Thu Sep 17 17:30:32 EST 2009


Dear Colleagues,

I'm looking for a "bpmap" file that maps Affymetrix Arabidopsis tiling array
1.0R probes onto the TAIR9 or TAIR8 genome sequence.

(This is for setting up a demonstration server that will show labs how they
can easily visualize and share tiling array and RNA-Seq data via the
Integrated Genome Browser (igb.bioviz.org) and DAS, one of the deliverables
for an NSF 2010 award, which started a year ago.)

The array corresponds to GEO platform accession GPL1980. (If this is wrong,
please let me know...the Web page for it is here:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1980)

The Web page for GPL1980 at GEO links to a bpmap file, but we are not yet
sure which genome it references. Probably it is the TAIR7 genome, but we
haven't tested it as yet. The bpmap file that Affymetrix distributes
references TAIR7 (what they call Jan 2004) and the company has no immediate
plans to update it because their tiling array support relies on a genome
being supported by the UCSC Genome Bioinformatics group, which only supports
animal and some fungal genomes.

If you know of anyone who has a bpmap file for the Arabidopsis Tiling 1.0R
Array for TAIR9, or even TAIR8, I would be very grateful if you would give
me their contact information or send me a link to the file.

Also, if you are looking for such a file, please let me know, and I'll get
in touch as soon as I find one...or as soon as we create it, if one cannot
be found.

Thank you very much for your time,

Ann Loraine
Associate Professor
Dept. of Bioinformatics and  Genomics
UNC Charlotte


More information about the Arab-gen mailing list