Question: Get MW of a protein given a uniprot ID in R
2
gravatar for kobipe3
4.8 years ago by
kobipe380
Israel
kobipe380 wrote:

I want to query the molecular weight of multiple proteins from R given uniprot ids. I thought of using biomaRt or UniProt.ws, but didn't see which field I should query.

There are online tools performing the calculation given a uniprot ID (PIR, ExPASy), but you have to manually enter the input and save the output.

I want the MW that appears in UniProt when looking in "Sequences" under Mass (for example for the entry http://www.uniprot.org/uniprot/Q9Z2Y8)

ADD COMMENTlink modified 4.8 years ago by me690 • written 4.8 years ago by kobipe380
2

Be aware that the calculated MW on the UniProt page does not include any PTM's. It is solely based on the AA sequence and may as well include signal peptides.

ADD REPLYlink written 4.8 years ago by koen20

Try with corresponding genome annotation package, like "org.Hs.eg.db" for human.

ADD REPLYlink written 4.8 years ago by juncheng180

Hello kobipe3!

We believe that this post is does not fit the main topic of this site.

Thanks for all the answers

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 4.8 years ago by kobipe380
2

Instead of closing your own question, please accept the correct answer(s), you may also vote to say thanks.

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Michael Dondrup46k
4
gravatar for me
4.8 years ago by
me690
Switzerland
me690 wrote:

On the uniprot site you can ask for the predicted mass column.

Click on the columns button. click on the check-box labeled mass under the sequence category.

Save, search for your accession using the syntax below and get tab delimited output back.

http://www.uniprot.org/uniprot/?format=tab&query=accession:Q6GZX4&columns=id,entry+name,mass

ADD COMMENTlink modified 20 months ago • written 4.8 years ago by me690
3
gravatar for Neilfws
4.8 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

You can get this information from the TogoWS REST service, starting from UniProt ID. For example, using PROSC_MOUSE (which is the ID, Q9Z2Y8 is the accession):

library(rjson)
library(RCurl)

u <- getURL("http://togows.dbcls.jp/entry/uniprot/PROSC_MOUSE.json")
j <- fromJSON(u)

j[[1]]$sq$MW

# [1] 30049

Conversion from accession to ID should be easy using R/biomaRt (search Biostar for numerous examples).

 

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Neilfws48k
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