R package to extract fasta sequence using gene names

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5.5 years ago

genetics101 • 0

I have hundreds of gene names like this: c("SS1G_03709", "SS1G_07286", "SS1G_06430"). I want to retrieve their nucleotide fasta sequence using R package from NCBI. Any suggestion?

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ADD COMMENT • link updated 5.4 years ago by Biostar 20 • written 5.5 years ago by genetics101 • 0

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Using R for such a task is over kill IMO. Use seqtk or seqkit or fasomerecords or grep (if you have sequences in single line).

ADD REPLY • link 5.5 years ago by cpad0112 21k

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Sorry, but I want to retrieve those sequences from NCBI.

ADD REPLY • link 5.5 years ago by genetics101 • 0

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you can use batch query on NCBI web interface or EBI web interface, NCBI eutils or Ensembl REST api or third party rest APIs for sequence retrieval.