Question: How to distinguish protein isoforms using biomaRt?
1
gravatar for richierocks
4.0 years ago by
richierocks10
United States
richierocks10 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 • 1.6k views
ADD COMMENTlink modified 4.0 years ago by shelly.deforte190 • written 4.0 years ago by richierocks10
4
gravatar for Emily_Ensembl
4.0 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

There is no canonical defined in BioMart.

ADD COMMENTlink written 4.0 years ago by Emily_Ensembl18k

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

ADD REPLYlink written 4.0 years ago by richierocks10

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

ADD REPLYlink written 4.0 years ago by Emily_Ensembl18k
1
gravatar for shelly.deforte
4.0 years ago by
United States
shelly.deforte190 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 COMMENTlink written 4.0 years ago by shelly.deforte190
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