[BiO BB] Affymetrix probe annotation- anyone need to identify unknowns?

Mike Marchywka marchywka at hotmail.com
Tue Jun 26 09:55:55 EDT 2007

I've developed a bunch of scripts specifically to track down speculative
annotations for unknown probe ID's from the Affymetrix canine array.
I've turned up a bunch of interesting things that compare
favorably to the annotations in their download files and web pages.

If anyone has any interest in evaluating the quality of these assignments
or knows of better approaches
I'd be happy to learn about them or run a few probe ID's and share my recent 
results and interact.
My process requires a list
of probe ID's that I can first run against their latest annotation download 
For those with unsatisfactory annotations, I run a more complicated blast 
( typically taking about 1 hour per probe set ) and a second script for 
pulling out
most reasonable matches. Personally I think I've found some very interesting 
but could obviously use more expert commentary and criticism.

It is now completely automated- give it a probe list, invoke 2 scripts, and 
back a hit list. But, it is specialized to canine data just due to the
Affymetrix files I have ( I need to known which annotation file to parse and
which web page to hit - both of these are hardcoded for dogs right now).
The results include names and numbers of most likely suspects, clustalw 
for these suspects, and lots of "raw data" including blast results, 
candidate fasta
files, etc. The blast search part in the first script I have reasonable 
for but the second part, automated hit extraction, is a lot more tentative.

Please reply either on or off list as you see fit.


Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
404-788-1216 (C)<- leave message
989-348-4796 (P)<- emergency only
marchywka at hotmail.com

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