How to convert ENSEMBL gene IDs to nucleotide sequences?
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4.7 years ago
harshraje19 ▴ 40

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

gene sequence sequencing rna-seq Assembly • 1.1k views
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4.7 years ago

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

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

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

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4.7 years ago
GenoMax 147k

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.

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

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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:

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