Question: R package to extract fasta sequence using gene names
0
gravatar for genetics101
17 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 • 962 views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 17 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 17 months ago • written 17 months ago by cpad011212k

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

ADD REPLYlink written 17 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 17 months ago • written 17 months ago by cpad011212k

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

ADD REPLYlink written 16 months ago by zx87549.1k
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