R package to extract fasta sequence using gene names
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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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).
Sorry, but I want to retrieve those sequences from NCBI.
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.
Related post: How do I loop over a list of gene symbols to extract sequences from NCBI?