How to extract all annotations in a genomic range from NCBI using R?
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2.1 years ago
Solowars ▴ 60

Hello all,

I want to study the genes in the neighbourhood of a number of genes of interest across multiple species. For several reasons, I chose to use NCBI annotations for this task, and I'm playing around with R and dedicated packages, such as rentrez, which can achieve many cool things.

However, I couldn't find a way to, for example, specify assembly, species, chromosome and search coordinates and get back a file (or a list for that matter) containing the corresponding gene annotations of all genes annotated in the specific region.

I wanted to know, in case somebody with more NCBI experience than me reads this, if this task is achievable using R tools or not (so I can invest my time searching for another way to do it).

NB.: I know that doing this should be relatively trivial using Ensembl and biomaRt, but I'd rather do it using NCBI, if possible.

Thank you so much for your thoughts and consideration.

Cheers,

R rentrez NCBI Synteny comparative genomics • 504 views
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