[BioC] XML data

Sean Davis sdavis2 at mail.nih.gov
Mon Jul 5 17:05:13 CEST 2004

You can get these from Affy at:


There are downloadable FASTA sequence files for hgu133a.  These need to be
prepared using the formatdb command that comes with the blast package from

Depending on how you want to think of your problem, it may make more sense
to blast these sequences against your sequences of interest (a more typical
analysis, I think).


On 7/5/04 10:39 AM, "S Peri" <biocperi at yahoo.com> wrote:

> Hi Group,
> I want to create a database of Affy probe sequences
> that can be used to BLAST (NCBI local BLAST) my
> sequence files against this database.  For this,  I
> downloaded the XML based  hgu133a (1.5.0)Human
> gzipped XML data from BioConductor.  The file
> extension is weird which is hgu133plus2.xml.gz.xml,
> this is not in gzipped format. When I try to open I
> can see XML tags and I do not see any sequence data.
> This looks like annotation data.
> Could any one please suggest which is the correct file
> that has the sequence data for all affy chips.  Also,
> is there some way to format that sequence data for
> NCBI BLASTable database.
> Thank you. 
> Cheers
> SP
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