Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: How to distinguish protein isoforms using biomaRt?
1
gravatar for richierocks
4.7 years ago by
richierocks • 10
United States
richierocks • 10 wrote:

I want to retrieve the canonical sequence for some proteins from ensembl, based upon their UniProt IDs.

library(biomaRt)

ensemblMart <- useMart(
  biomart = "ensembl",
  dataset = "hsapiens_gene_ensembl"
)

(result <- getBM(
  attributes = c("uniprot_swissprot", "peptide"),
  filters    = "uniprot_swissprot",
  values     = "P31749",
  mart       = ensemblMart,
  bmHeader   = TRUE
))

This particular protein has two isoforms, both of which are returned.  I only care about the canonical form, so how can I distinguish the isotopes?

I suspect that I need to return another of the attributes from the mart

listAttributes(ensemblMart)

but I don't know which one.

 

 

 
biomart R • 1.9k views
ADD COMMENT • link •
modified 4.7 years ago by shelly.deforte • 190 • written 4.7 years ago by richierocks • 10
4
gravatar for Emily_Ensembl
4.7 years ago by
Emily_Ensembl ♦ 20k
EMBL-EBI
Emily_Ensembl ♦ 20k wrote:

There is no canonical defined in BioMart.
ADD COMMENT • link written 4.7 years ago by Emily_Ensembl ♦ 20k

Thanks.  Just to be clear: are there any other ways of distinguishing isoforms?

ADD REPLY • link written 4.7 years ago by richierocks • 10

You could perhaps use the APPRIS principal isoform, which is available from BioMart.

ADD REPLY • link written 4.7 years ago by Emily_Ensembl ♦ 20k
1
gravatar for shelly.deforte
4.7 years ago by
shelly.deforte • 190
United States
shelly.deforte • 190 wrote:

If you are trying to retrieve protein sequences using UniProt IDs, why not just fetch them directly from UniProt using something like urllib2 on Python (I'm sure there's a way to do this in R as well)? Or even just wget on linux, ie. wget -nv http://www.uniprot.org/uniprot/O53166.fasta.  UniProt will return the canonical sequence.
ADD COMMENT • link written 4.7 years ago by shelly.deforte • 190
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 788 users visited in the last hour