In case you aren’t on the UCSC announcement mailing list, and you don’t go to the site via their homepage with the posted news–you should know about this new tool at the UCSC Genome Browser. It will take variations that you are exploring and make a prediction about whether the variant is associated with a function, and potentially if it is damaging to a protein. It’s under active development, so try it out. And if there are features you could use, suggest them. See the VAI page for more.
Here are the details via their email, but sign up for the “announce” mailing list to get this news like this in your inbox if you like too:
In order to assist researchers in annotating and prioritizing thousands
of variant calls from sequencing projects, we have developed the Variant
Annotation Integrator (VAI). Given a set of variants uploaded as a
custom track (in either pgSnp or VCF format), the VAI will return the
predicted functional effect (e.g., synonymous, missense, frameshift,
intronic) for each variant. The VAI can optionally add several other
types of relevant information, including: the dbSNP identifier if the
variant is found in dbSNP, protein damage scores for missense variants
from the Database of Non-synonymous Functional Predictions (dbNSFP), and
conservation scores computed from multi-species alignments. The VAI also
offers filters to help narrow down results to the most interesting variants.
Future releases of the VAI will include more input/upload options,
output formats, and annotation options, and a way to add information
from any track in the Genome Browser, including custom tracks.
There are two ways to navigate to the VAI: (1) From the “Tools” menu,
follow the “Variant Annotation Integrator” link. (2) After uploading a
custom track, hit the “go to variant annotation integrator” button. The
user’s guide is at the bottom of the page, under “Using the Variant
As always, we welcome questions and feedback on our public mailing list:
UCSC Genome Bioinformatics Group