Question: Retrieve multiple FASTA from UniProt using R
0
gravatar for akansha.gitanjali
24 days 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 • 124 views
ADD COMMENTlink modified 23 days ago by h.mon28k • written 24 days 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 24 days ago by h.mon28k

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 23 days ago by genomax75k • written 24 days ago by akansha.gitanjali10
1

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 24 days ago by h.mon28k
0
gravatar for h.mon
23 days ago by
h.mon28k
Brazil
h.mon28k 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 written 23 days ago by h.mon28k
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: 1002 users visited in the last hour