Question: How to convert ENSEMBL gene IDs to nucleotide sequences?
0
gravatar for harshraje19
8 weeks ago by
harshraje1920
harshraje1920 wrote:

Hello Everyone, I hope everyone is in good health.

I want to convert ensembl gene ids to nucletide sequences?

Can anyone suggest me tool or software or command line in linux or R to do so?

I have follwoing IDs from plant Vitis Vinifera

VIT_00s0187g00200 VIT_00s0187g00250 VIT_00s0194g00310 VIT_00s0256g00080 VIT_00s0341g00060 VIT_00s0561g00020 VIT_00s0838g00020 VIT_01s0010g00340 VIT_01s0010g00520 VIT_01s0010g01260 VIT_01s0011g00940 VIT_01s0011g03080 VIT_01s0150g00550 VIT_02s0012g00350 VIT_03s0038g02910 VIT_03s0091g00430 VIT_04s0008g00760 VIT_04s0023g01620 VIT_04s0023g01830 VIT_05s0077g02200 VIT_05s0094g00440 VIT_06s0004g06920 VIT_06s0004g08120 VIT_06s0009g02210 VIT_06s0080g00260 VIT_07s0005g00540 VIT_07s0005g01530

Thanks

ADD COMMENTlink modified 8 weeks ago by genomax84k • written 8 weeks ago by harshraje1920
3
gravatar for Jean-Karim Heriche
8 weeks ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k wrote:

For a small number of IDs, try the EnsemblPlants Biomart otherwise, you have the perl API.

ADD COMMENTlink written 8 weeks ago by Jean-Karim Heriche22k

I have many files with gene IDs. How to use perl API? Is there any command? Can you please elaborate. Thanks

ADD REPLYlink written 8 weeks ago by harshraje1920

Link @Jean-Karim included shows how to use API.

ADD REPLYlink written 8 weeks ago by genomax84k
3
gravatar for genomax
8 weeks ago by
genomax84k
United States
genomax84k wrote:

Strictly speaking those are not Ensembl ID's. You can download the CDS sequences file from Ensembl plant web site for the grape genome. That file should contain those sequences.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by genomax84k

After downloading the CDS file from ensembl plant web site, how to filter specific gene IDs? Is there any specific command.

ADD REPLYlink written 8 weeks ago by harshraje1920
1

Linearize fasta sequences, grep(-f file with your ID's) for the ID's you need and then convert the sequences back to fasta format.

Code for first and last part available from @Pierre here:

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by genomax84k
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