[ensembl-dev] BIOMART segment(SNP) query

[Rhoda Kinsella]

Hi Matthias
If you wish to use Biomart you will need to perform two queries where  
you get the coordinates of your snps that you want to use as start and  
end regions and then put these start and end positions into a second  
query using the base pair start and end filter. It may be easier to  
use the API from variation and core to get this information. Please  
let us know if you require help with the API.
Regards
Rhoda


On 15 Mar 2011, at 09:11, Matthias Macé wrote:

> Dear all,
> First thank you for any suggestion.
> We are trying to get genes overlapping with segments comprised  
> between two SNPs.
> Input = rsID from start snp, rsID for end snp (as shown below).
> Expected output : gene IDs
>
> Example:
> query:            rs_ID_1---------------------------rs_ID_2
> <-----------gene_1------------->
>                                         <-------gene_2--------->
>
> <-----------gene_3------------->
>
> It would return : gene_1, gene_2, gene_3
>
> We would like to perform this in a unique query (e.g. not with a  
> first query SNP >> coordinates followed by a second coordinates >>>  
> genes).
>
> We tried this using Biomart (db=Homo sapiens Variation (dbSNP  
> 132;ENSEMBL); Filters: REGION/Marker-end-start; Attributes: any ID)  
> without success (it returns a null output). In a general way,  
> nothing happens when using this filter.
>
> So here comes our questions:
> - how to use this filter ?
> - do you have any suggestion for doing this ?
>
>
> Best regards,
> MM
>
>
> -- 
> "Only two things are infinite, the universe and human stupidity, and  
> I'm not sure about the former." -Albert Einstein
> Dr Matthias Macé, DVM, PhD
> INSERM U1043
> C.H.U. Purpan - BP 3028
> 31024 TOULOUSE CEDEX 3
> tel: (33) 562 74 45 09
> mobile: (33) 608 881481
> http://www.u563.toulouse.inserm.fr/
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

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