Hello, Danit,
I'd like to add to what Brooke said.
If I understand your question properly, you should be able
to check your SNP location on a different assembly using the
Convert link at the top of the page.
E.g., If your SNP is this region on the hg19 assembly:
chr21:33,036,131-33,036,218
and you want to see it in hg18, the Convert link takes you to:
chr21:31,958,002-31,958,089
Note that the gene is the same (SOD1) but the coordinates have
shifted by 1.1 million bases. This can often happen because the
estimated size of a feature such as a telomere or centromere
(which are not typically sequenced) may have changed between
assemblies. The sequences of regions that =have= been thoroughly
sequenced are not changing very much between assemblies anymore,
though the coordinates often do.
You can convince yourself that you are in the right place by
grabbing the sequence via the DNA link and using blat on the
other assembly to confirm that the coordinates have changed but
the sequence has not.
regards,
--b0b kuhn
ucsc genome bioinformatics group
On 6/29/2011 12:42 PM, Brooke Rhead wrote:
> Hi Danit,
>
> The builds are not expected to have the same sequence at the exact same
> coordinates. The hg19 build is newer than the hg18 build. There are
> links to much more information on both builds on the gateway page of the
> Genome Browser:
> http://genome.ucsc.edu/cgi-bin/hgGateway
> (select either assembly and scroll down)
>
> For your SNP, you will need to find out which build coordinates were
> used to find/report the SNP.
>
> I hope this is helpful. If you have further questions, please send them
> to [email protected].
>
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
>
>
> On 06/29/11 06:18, Danit Oz-Levi wrote:
>> Hello,
>> I have aproblem regarding the different ucsc builds- hg18 and hg 19.
>> For hg18,In a certain location in the genome, the reference is G. For hg19-
>> same exact location, reference is C. the amino acid is also changed between
>> versions- from R to P. How can I know which one is more accurate? how can I
>> tell whether I have a SNP in a patient if I compare it to the ref in hg19
>> and I get a SNP, but in hg18 the patient has the normal genotype?
>>
>> I would highly appriciate your help.
>>
>> Thanks
>> Danit
>>
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