Downloading gene sequences for a list of genes using E-utilities
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3.8 years ago
Bioinfonext ▴ 460

Hi,

Could you please help how I can download nucleotide fasta sequences for a list of the gene using E-utilities or any other way? I have tried batch entrez but it is very slow and taking lots of time.

BGIOSGA013239
BGIOSGA028856
BGIOSGA017372
BGIOSGA022107
BGIOSGA032186
BGIOSGA035117
BGIOSGA036507
BGIOSGA004130
BGIOSGA033191
BGIOSGA032684
BGIOSGA024392
BGIOSGA000752
BGIOSGA031854
BGIOSGA019027
BGIOSGA005053
BGIOSGA026092
BGIOSGA001652
BGIOSGA036579
BGIOSGA004321
BGIOSGA022597
BGIOSGA026268
BGIOSGA018579
BGIOSGA017484
BGIOSGA009189
BGIOSGA008622
BGIOSGA024943

Many thanks

RNA-Seq linux ncbi bash genome • 862 views
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What kind of ID's are these? They bring up no hits at all at NCBI.

Note: It looks like these are some kind of Rice sequence ID's but since they are non standard you will need to either translate them to something in NCBI OR get the fasta sequence from this LINK (which a google search brought up at floresta.eead.csic.es).

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Have you tried biomart at ensembl plants? I was able to download gene sequences of the ids you provided by choosing Oryza sativa indica group as the plant. Biomart can also be accessed in R if you want to put this inside a script.

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3.8 years ago
ashish ▴ 680

Most probably these are ids from Oryza sativa indica which is a different sub-species than the one we see more often (japonica). It was sequenced by BGI, China and the assembly is available at ensembl plants which can be accessed using biomart. However, BGI has sequenced many other plants and we will have to wait for the OP to update on the organism name.

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Yes , these are Oryza sativa indica gene sequences Id, I think biomart will be ideal to get the gene sequences.

Many thanks

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