Question: How to get gene sequences from gene IDs from different organisms?
0
gravatar for Ali R. Vahdati
3.9 years ago by
Zurich, Switzerland
Ali R. Vahdati190 wrote:

Hi,

I have a list of Ensembl gene IDs from different organisms and I would like to retrieve their sequences. I had used Biomart before, but it requires to specify the organism before one can download the gene sequences of a specific gene ID. This would not be feasible because I do not know which organism each gene belongs to, unless I search the gene ID.

Is there any solution to this problem that does not require me to learn Perl? I know Python.

 

Thanks in advance

retrieve sequence ensembl • 1.2k views
ADD COMMENTlink modified 3.9 years ago by Emily_Ensembl17k • written 3.9 years ago by Ali R. Vahdati190

Can you post some example ids? Be cause few people (like me) are not familiar with these formats.

ADD REPLYlink written 3.9 years ago by venu6.0k

Yes the gene IDs are from different organisms, such as ENSG00000234547 in human, or ENSMUSG00000097570 in mouse.

ADD REPLYlink written 3.9 years ago by Ali R. Vahdati190

Doesn't Ensembl gene IDs contain organism info? For example: 

  • Danio rerio - ENSDAR
  • Rattus norvegicus - ENSRNO
  • Mus musculus - ENSMUS
  • Gallus Gallus - ENSGAL
  • Bos taurus ENSBTA
ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by PoGibas4.7k

True, but there are so many genes I cannot find their organisms manually. If there is a table for that it would help

ADD REPLYlink written 3.9 years ago by Ali R. Vahdati190
3
gravatar for Emily_Ensembl
3.9 years ago by
Emily_Ensembl17k
EMBL-EBI
Emily_Ensembl17k wrote:

You can use the Sequence ID endpoint from the Ensembl REST API, which you can access in any programming language. Here's an example client for the REST API (not this endpoint) in Python.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Emily_Ensembl17k

Thanks. This exactly answers the question.

ADD REPLYlink written 3.9 years ago by Ali R. Vahdati190

http://rest.ensembl.org/sequence/id/ENSG00000234547? , Does this mean there is no sequence with this id? or anything went wrong? In one of the comments OP has mentioned 2 ids, id in the link is from humans and the other one (ENSMUSG00000097570) is from mouse for which I can find the sequence.

ADD REPLYlink written 3.9 years ago by venu6.0k
1

I had mistyped the gene ID. That gene ID does not exist, but the correct address would be this: http://rest.ensembl.org/sequence/id/ENSG00000234745?

ADD REPLYlink written 3.9 years ago by Ali R. Vahdati190
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