Downloading Sequences From Ensembl Using Ids

Question

[jaip217]

Hi Everyone,

Quick question: Does anyone know how to download a batch of sequences from Ensembl using their Ensembl Identifiers? I know I can do this using the Perl API but I would like to avoid doing this. I have .csv file I got from Ensembl but I can't figure out how to download them.

Thanks in advance!

Answer 1

[kandoigaurav]

Have you tried using the Biomart (http://www.ensembl.org/biomart/martview/6e0b7f8b692454fdd5a5417af2de147c) interface for batch queries?

[Emily]

There's a help video here.

Answer 2

[Laura Luebbert]

You can use gget seq:

Terminal:

pip install gget
gget seq ENSG00000034713 ENSG00000104853 ENSG00000170296

Python:

!pip install gget
import gget
gget.seq(["ENSG00000034713", "ENSG00000104853", "ENSG00000170296"])

This returns sequences of the passed genes in FASTA format.

Answer 3

[dukecomeback]

Biomart restricts on species, for multiple id from different species, check here: https://rest.ensembl.org/documentation/info/sequence_id