How to get gene sequences from gene IDs from different organisms?
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6.7 years ago

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

sequence retrieve ensembl • 1.8k views
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Can you post some example ids? Be cause few people (like me) are not familiar with these formats.

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

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

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6.7 years ago
Emily 23k

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.

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Thanks. This exactly answers the question.

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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.

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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?

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