This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to get gene sequences from gene IDs from different organisms?

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

ensembl sequence
• 3,774 views • link
updated by Ram Ram • written by Ali R. Vahdati Ali R. Vahdati

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

• 0 views • link
written by venu venu

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

• 0 views • link
written by Ali R. Vahdati Ali R. Vahdati

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
• 0 views • link
updated by Ram Ram • written by PoGibas PoGibas

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

• 0 views • link
written by Ali R. Vahdati Ali R. Vahdati

1 answer

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.

• 0 views • link
updated by Ram Ram • written by Emily Emily

Thanks. This exactly answers the question.

• 0 views • link
written by Ali R. Vahdati Ali R. Vahdati

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.

• 0 views • link
updated by Ram Ram • written by venu venu

Log in to answer this question.

More posts like this