Dear all,
I have a list of taxa for which I would like to download the gene sequences for a specific gene (e.g. 28S gene) from NCBI. Is there an easy way to do a batch download or do I have to do it one by one if I do not have the NCBI Genbank accession numbers? I know there are the E-Utilities from Entrez but so far my attempts failed. Is there any other useful tool/script? Maybe for R?
Thanks a lot in advance,
Belinda
Hi Belinda,
that's what NCBIs Eutils are designed for. There are various implementations, I have attached an example of getting accession numbers from taxon names with the R package rentrez (https://cran.r-project.org/web/packages/rentrez/index.html). Hope this helps.
Michael
Dear Michael,
yes I already tried the NCBI E-utilities using Linux but always encountered some errors. The R code looks good & much easier to use- thanks a lot!!!
That really simplifies things!
Best wishes,
Belinda
When the batch entrez was for some reason failing I used the batch download via the browser. It's the third option from here: https://edwards.sdsu.edu/research/ncbi-sequence-or-fasta-batch-download-using-entrez/
You can use NSDPY package directly from the terminal. Based on an NCBI query it downloads the batch of sequences and can filter the sequences based on gene annotations or taxonomic information:
https://pypi.org/project/nsdpy/
ReadTheDoc:
https://nsdpy.readthedocs.io/en/latest/main.html#overview
The related paper:
https://authors.elsevier.com/sd/article/S235271102200036X
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