[ensembl-dev] determining consequences of SNPs

Andrea Edwards edwardsa at cs.man.ac.uk
Tue Mar 22 19:41:52 GMT 2011


To clarify, does this mean that the following process occurs:

1. Naturally mRNA sequences can have different sequences between 
individuals due to sequence variation and complications like polyA tails etc
2. Do you map mRNA sequences to the reference genome to get a consensus 
of the genomic cordinates for the mRNA from the different mRNAS
3. Then you store a single mRNA sequence based on the consensus genomic 
coordinates and the underlying reference sequence template
4. Then you calculate SNP consequences based on the canonical transcript 
sequence

I am interested because other data sources don't operate like this and I 
want to be sure of the difference.

thanks a lot

On 18/03/11 23:34, Fiona Cunningham wrote:
> Hi Andrea,
>
> We use the genomic coords from the reference assembly for the
> consequences. (and also to build all our genes so the Ensembl
> transcripts are the same. )
> Fiona
>
> ------------------------------------------------------
> Fiona Cunningham
> Ensembl Variation Project Leader, EBI
> www.ensembl.org
> www.lrg-sequence.org
> t: 01223 494612 || e: fiona at ebi.ac.uk
>
>
>
> On 18 March 2011 20:06, Andrea Edwards<edwardsa at cs.man.ac.uk>  wrote:
>> Hello
>>
>> When ensembl calculates the consequence of an exonic SNP as
>> synonymous/non-synonmous etc, does it use the genomic sequence or mRNA
>> sequences. I believe the former is more accurate as mRNA sequences can
>> different from the genomic sequence?
>>
>> thanks a lot
>>
>> _______________________________________________
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>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
>>





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