Question: R package to extract fasta sequence using gene names
0
gravatar for genetics101
6 months ago by
genetics1010 wrote:

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?

R • 499 views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 6 months ago by genetics1010
2

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 REPLYlink modified 6 months ago • written 6 months ago by cpad011211k

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

ADD REPLYlink written 6 months ago by genetics1010
2

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.

ADD REPLYlink modified 6 months ago • written 6 months ago by cpad011211k

Related post: How do I loop over a list of gene symbols to extract sequences from NCBI?

ADD REPLYlink written 5 months ago by zx87547.3k
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