[Genome] Extracting exons corresponding to affymetrix probes

[Kayla Smith]

Schraga,

The short answer is No.  We do not have tools to give you the data in 
the format you are asking.  We host data and have some tools for 
extracting subsets of it, but what you're looking to do is going to 
require you to write a program to process the data to get what you want.

I can however mention some tools that you may find useful:

-You can use the Table Browser to make a custom track of all of the 
exons of a given track.   You could extract the sequence from each item 
in this custom track.

-You can look at our table affyHuEx1.  This table has the coordinates of 
where the consensus sequences for each probe on the Affy Human Exon 
array mapped to the genome.

-You can use the intersection tool in the Table Browser to intersect the 
coordinates of two tables.  You may find that intersecting the two 
tables mentioned above provides information that is useful to you.

Here is a link to the users guide for the Table Browser:
http://genome.ucsc.edu/cgi-bin/hgTables?db=hg18#Help

Finally, the Galaxy website, http://main.g2.bx.psu.edu/ has more 
advanced data manipulation tools than we have here on the Genome 
Browser.  You might find something useful there.

Affymetrix has some information on this array here:
http://www.affymetrix.com/products/arrays/specific/exon.affx
Realize that there are approximately four probes per exon and roughly 40 
probes per gene.

If you are interested in help on any of the topics I've listed above, 
please write back and I can help you work through them.

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smtih
UCSC Genome Bioinformatics Group




Schraga Schwartz wrote:
> Hello,
> 
>  
> 
> I would like to extract the full exons corresponding to the affymetrix human
> exon probeset. In addition, I'd like to extract the introns flanking these
> exons. 
> 
>  
> 
> In other words, I currently have a list of such probes, within exons, and I
> would like to find out the full exonic sequences (and flanking introns), by
> crossing the probe coordinates with coordinates of mRNAs and ESTs. How can I
> best do this, using UCSC? Is there an inbuilt option?
> 
>  
> 
> Thank you very much,
> 
>  
> 
> Schraga Schwartz
> 
> Department of Human Molecular Genetics and Biochemistry,
> Tel Aviv University Medical School,
> Tel Aviv 69978, Israel.
> Tel: +972-3-640 6894
> 
> email: schragas at post.tau.ac.il
> 
>  
> 
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