How to convert ENSEMBL gene IDs to nucleotide sequences?

Question

[harshraje19]

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

Answer 1

[Jean-Karim Heriche]

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

[harshraje19]

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

[GenoMax]

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

Answer 2

[GenoMax]

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.

[harshraje19]

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

[GenoMax]

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:

Linearize a fasta sequence

awk -f linearizefasta.awk < input.fa

or

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.fa

Format back to fasta

tr "\t" "\n" < linearized.tsv

if you know your fasta header have a length < 60

tr "\t" "\n" < linearized.tsv | fold -w 60

view raw README.md hosted with ❤ by GitHub

	/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;}
	{printf("%s",$0);}
	END {printf("\n");}

view raw linearizefasta.awk hosted with ❤ by GitHub