complete genomes retrieval using R

Question

[sadiraja19]

how can i download complete genomes for pseudomonas aeruginosa from genbank using R

[sadiraja19]

i hv biomart but need a code which i dnt hv

[Nicolas Rosewick]

What did you try ? Sorry to be rude but we're not here to do your homework...

[sadiraja19]

yes i did not ask for my home work i amnot a bioinformatician i am trying to download 89 seudomonas aeruginosa genomes fromgenbankin fasta formate.i have tried doin it using biomartr in R but not working

Answer 1

[caggtaagtat]

Hi,

check out the package "BiomaRt", which holds functions to access genomes from ensembl, wormbase, cosmic, and gramene. I think ensembl does not have an pseudomonas genome, so you should try wormbase maybe.

Link to the package: https://bioconductor.org/packages/release/bioc/html/biomaRt.html

Link to vignette: https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html

[sadiraja19]

i need to download from genbank plz in fasta

[GenoMax]

I think ensembl does not have an pseudomonas genome, so you should try wormbase maybe.

Pseudomonads are bacteria and won't be in wormbase (which pertains to a nematode, C.elegans).

[caggtaagtat]

ups yeah, you're right^^

Answer 2

[GenoMax]

Not a solution in R but you could use this utility to download the genomes you need [ncbi-genome-download]. There are other ways of doing this but this may be the easiest.