[ensembl-dev] Ensemble Search Help

[Bradley Ross]

Hello Ben,


My apologies the sequence is supposed to be AGGTCANAGGTCA. I forgot to repeat it in the last email.


For example, I know the above sequence should be located in the adipocyte fatty-acid binding protein 2 (AP2). Could you conduct the same search (keeping in mind to move the start location back at least 20kb) and tell me whether or not you find the sequence through ensemble?


Brad

________________________________
From: Dev <dev-bounces at ensembl.org> on behalf of Ben Moore <bmoore at ebi.ac.uk>
Sent: June 7, 2017 5:16:47 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] Ensemble Search Help

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

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) and navigate to the ‘Region in Detail’ page (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<mailto: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

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<mailto:dev-bounces at ensembl.org>> on behalf of Ben Moore <bmoore at ebi.ac.uk<mailto: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<mailto: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<mailto:bmoore at ebi.ac.uk>
+44 (0)1223 494265

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