Downloading Sequences From Ensembl Using Ids
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8.8 years ago
jaip217 ▴ 30

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!

ensembl • 4.3k views
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8.8 years ago
kandoigaurav ▴ 150

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

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2.3 years ago
dukecomeback ▴ 40

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

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8 weeks ago

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.

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