Question: Retrieve multiple FASTA from UniProt using R
0
gravatar for akansha.gitanjali
6 months ago by
akansha.gitanjali10 wrote:

I have a huge list of UniProt protein accession numbers and I need to retrieve the FASTA sequences from UniProt website. Is there any R script for doing that? I know I can do it from UniProt website but this will be used for further developing script for downstream mass spec analysis.

uniprot R fasta • 646 views
ADD COMMENTlink modified 6 months ago by h.mon29k • written 6 months ago by akansha.gitanjali10
1

See if this example from biomartr can help:

Example Retrieval Uniprot

Also, the Rcpi BioConductor package has a getFASTAFromUniProt() function.

ADD REPLYlink written 6 months ago by h.mon29k

Yes I can download whole proteome from Example Retrieval Uniprot. But I want to use different uniprot identifiers like ..................

ids <- c("P62754", "Q8K094", "Q64337")

I am using R 3.6.1 which doesn't support BioConductor. What to do?
> install.packages("bioconductor")
Installing package into ‘C:/Users/Gita/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified)
Warning in install.packages :   package ‘bioconductor’ is not available (for R version 3.6.1)
ADD REPLYlink modified 6 months ago by genomax84k • written 6 months ago by akansha.gitanjali10
2

BioConductor is a repository, not a package. The Rcpi link above has clear install instructions:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Rcpi")
ADD REPLYlink written 6 months ago by h.mon29k
1
gravatar for h.mon
6 months ago by
h.mon29k
Brazil
h.mon29k wrote:

Install Rcpi (I suggest using conda, as it can be a bit of a pain to install) and then, under R:

library( Rcpi )
fastas <- getFASTAFromUniProt( c( "P62754", "Q8K094", "Q64337" ) )
write( x, "uniprot.fasta" )
ADD COMMENTlink modified 13 days ago • written 6 months ago by h.mon29k
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