[ensembl-dev] Ensemble Search Help

Ben Moore bmoore at ebi.ac.uk
Wed Jun 7 10:16:47 BST 2017


Hi Brad,

I’m not sure exactly what you mean by the sequence not being revealed. However, when I search this genomic region in Ensembl I arrive at the following 'Region in Detail’ page:
http://www.ensembl.org/Homo_sapiens/Location/View?r=10:87763438-87971930;db=core <http://www.ensembl.org/Homo_sapiens/Location/View?r=10:87763438-87971930;db=core>

Once on this page, you can click on the blue ‘Export data’ button on the left hand side of the page, which opens a pop up window where you can select the type of data you want to download from this genomic region. By default, you will download the FASTA sequence. If you select the default parameters and download the FASTA sequence (which I have done, attached), you will be able to search this genomic sequence for your sequence of interest. I have found that ‘AGGTCA’ occurs multiple times in this sequence.

As a side note, you are able to search directly in Ensembl for the PTEN gene (http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000171862;r=10:87863113-87971930 <http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000171862;r=10:87863113-87971930>) and navigate to the ‘Region in Detail’ page (http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000171862;r=10:87863113-87971930 <http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000171862;r=10:87863113-87971930>), if that helps you find the relevant genomic region(s) for you study.

I hope these directions help you find the data you need, but please do get back in touch if you have any further questions.

Best wishes

Ben



> On 6 Jun 2017, at 20:12, Bradley Ross <1br6 at queensu.ca> wrote:
> 
> Hello, 
> 
> I am searching the human GRCh38.p10 through ensembl. For example I search the location of the PTEN gene according to the locations given by the NIH site:https://ghr.nlm.nih.gov/gene/PTEN#sourcesforpage <https://ghr.nlm.nih.gov/gene/PTEN#sourcesforpage>
> According to that site, the PTEN location is 10:87,863,438-87,971,930. 
> 
> I then entered the above location onto the ensembl GRCh38.p10 browser but changed the first number to 87,763,438 to move more upstream. Within the new region of 10:87,763,438-87,971,930, the sequence AGGTCA should be found but it is not revealed on the ensembl. 
> 
> Brad
> From: Dev <dev-bounces at ensembl.org> on behalf of Ben Moore <bmoore at ebi.ac.uk>
> Sent: June 6, 2017 10:21:31 AM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] Ensemble Search Help
>  
> Hi Brad,
> 
> We can definitely try and help you. You can get help through this mailing list, or you can send further information to helpdesk at ensembl.org <mailto:helpdesk at ensembl.org>, which will create a ticket in our helpdesk system, where a member of the Ensembl team will help you directly. In any case, we’d need to know some more information:
> - which species are you searching? which genome assembly are you using in your work?
> - do you have an example set of genomic coordinates that you have used?
> - what do you see (screenshot)? What do you expect to see?
> 
> Best wishes
> 
> Ben
> 
>> On 6 Jun 2017, at 15:15, Bradley Ross <1br6 at queensu.ca <mailto:1br6 at queensu.ca>> wrote:
>> 
>> Hello,
>> 
>> I was wondering if there was someone I could contact regarding using the genome browser Ensembl. 
>> 
>> I have searched specific regions where I know a particular sequence should be located, but it does not come up when I search through this genome browser. 
>> 
>> Any assistance would be greatly appreciated. 
>> 
>> Brad
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org>
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> Ben Moore
> Ensembl Outreach Officer
> 
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> UK
> 
> bmoore at ebi.ac.uk <mailto:bmoore at ebi.ac.uk>
> +44 (0)1223 494265
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

Ben Moore
Ensembl Outreach Officer

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

bmoore at ebi.ac.uk
+44 (0)1223 494265

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