Question: complete genomes retrieval using R
0
gravatar for sadiraja19
2.2 years ago by
sadiraja190
sadiraja190 wrote:

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

R genome • 706 views
ADD COMMENTlink modified 2.2 years ago by genomax78k • written 2.2 years ago by sadiraja190

i hv biomart but need a code which i dnt hv

ADD REPLYlink written 2.2 years ago by sadiraja190

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

ADD REPLYlink written 2.2 years ago by Nicolas Rosewick8.6k

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

ADD REPLYlink written 2.2 years ago by sadiraja190
0
gravatar for caggtaagtat
2.2 years ago by
caggtaagtat930
caggtaagtat930 wrote:

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

ADD COMMENTlink written 2.2 years ago by caggtaagtat930

i need to download from genbank plz in fasta

ADD REPLYlink written 2.2 years ago by sadiraja190

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).

ADD REPLYlink written 2.2 years ago by genomax78k

ups yeah, you're right^^

ADD REPLYlink written 2.2 years ago by caggtaagtat930
0
gravatar for genomax
2.2 years ago by
genomax78k
United States
genomax78k wrote:

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.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by genomax78k
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