Question: complete genomes retrieval using R
0
gravatar for sadiraja19
16 months ago by
sadiraja190
sadiraja190 wrote:

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

R genome • 527 views
ADD COMMENTlink modified 16 months ago by genomax65k • written 16 months ago by sadiraja190

i hv biomart but need a code which i dnt hv

ADD REPLYlink written 16 months ago by sadiraja190

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

ADD REPLYlink written 16 months ago by Nicolas Rosewick7.5k

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 16 months ago by sadiraja190
0
gravatar for caggtaagtat
16 months ago by
caggtaagtat500
caggtaagtat500 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 16 months ago by caggtaagtat500

i need to download from genbank plz in fasta

ADD REPLYlink written 16 months 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 16 months ago by genomax65k

ups yeah, you're right^^

ADD REPLYlink written 16 months ago by caggtaagtat500
0
gravatar for genomax
16 months ago by
genomax65k
United States
genomax65k 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 16 months ago • written 16 months ago by genomax65k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1790 users visited in the last hour