[ensembl-dev] [External] Re: Obtaining the genomic sequences for all the 5'UTR and CDS for mouse genome

[Eric Engelhard]

Hello Allan,

The recommended methods for accessing genome wide feature annotations and  sequences are through either the Ensembl BioMart or by creating a local MySQL database and using the Perl API.

BioMart (https://useast.ensembl.org/biomart/martview) provides the easier query method and does not require scripting. You will want to select the “Ensembl Genes 112” database and the “Mouse Genes (GRCm39)” dataset and then select the attributes from “Features” and “Sequences” that meet your requirements.

Cheers!
Eric



Regeneron - Internal
From: Dev <dev-bounces at ensembl.org> On Behalf Of Allan Kamau
Sent: Wednesday, September 11, 2024 7:17 AM
To: dev <dev at ensembl.org>
Subject: [External] Re: [ensembl-dev] Obtaining the genomic sequences for all the 5'UTR and CDS for mouse genome

In short, is there a way to download the 5' UTR and the CDS sequences of the mouse genome? Any update will be appreciated. -Allan. On Tue, Sep 10, 2024 at 4: 03 PM Allan Kamau <kamauallan@ gmail. com> wrote: I would like to obtain the

In short, is there a way to download the 5' UTR and the CDS sequences of the mouse genome?

Any update will be appreciated.

-Allan.

On Tue, Sep 10, 2024 at 4:03 PM Allan Kamau <kamauallan at gmail.com<mailto:kamauallan at gmail.com>> wrote:
I would like to obtain the sequences for the 5' UTR and CDS for the mouse genome.
I began by filtering all the records having "five_prime_UTR" from the chromosome.<chromosome_name>.gff3.gz files from "https://ftp.ensembl.org/pub/release-112/gff3/mus_musculus/<https://urldefense.com/v3/__https:/ftp.ensembl.org/pub/release-112/gff3/mus_musculus/__;!!ODpDvJZr5w!A6FsD3BVS3WGT6ZFBpdbTtPlpVguweDG6V3d61yHHrFf8S0p4KRvTa6jt4dmfY7IV6hWw_RVScMolk9envpjnnE0$>", I obtain some 95358 records, it seems this number is too high as mouse genome has approximately 25,000 genes.

I did the similar filtering for records having the value "CDS" as their third field and obtained some 522159 entries, which is a large number considered there are only 25,000 genes for the GRCm39 genome.

What would be preferred way to obtain the 5' UTR and CDS for the entire mouse genome?

Regards,
-Allan.


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