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Old 10-03-2010, 09:49 AM   #3
cliff
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Join Date: Oct 2009
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Quote:
Originally Posted by svl View Post
One option (but perhaps not the most complete) is to use the Ensembl SnpEffectPredictor script:
ftp://ftp.ensembl.org/pub/misc-scrip...predictor_1.0/

There is also an online version (mirror site, because their main site is down):
http://useast.ensembl.org/tools.html

Both will annotate your variants (eg chr:1 123456 A/T) with their effect (eg NON_SYNONYMOUS, but also SPLICE_SITE and ESSENTIAL_SPLICE_SITE)

This is the list with types it will return:
http://useast.ensembl.org/info/docs/...ion/index.html

/svl
Thanks! Do you know if there is any script or online tool that can deal with data downloaded from UCSC? I am concerned with the possible conflict of the format or coordinate between ensembel and UCSC.
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