Convert Refseq Mrna Id To Swiss Prot Accession Ids

Question

[prajwalnj]

Hello,

I have several human ( about 5000) refseq ids, both protein (NP_xx) and nucleotide (NM_xx) and I am trying to convert them to swissprot accession ids.

I tried using Biomart id converter as well as UCSC table browser but I do get conversions for atleast a 1000 ids.

When I try to enter these ids individually into the Gene card website, it does have a swiss prot id.

Is there any tool or any solution to retrieve the remaining IDs ?

Thank you.

Answer 1

[Emily]

Hello

BioMart gets a bit grumpy with large datasets. It just stops working when it has too many values, and gives output for only those it managed to convert. Unfortunately, there doesn't seem to be a way to add a warning when it does this. And there isn't a definitive cut-off for when it starts doing this, so we can't even give people a limit (we now have an arbitrary and quite conservative limit of 500 IDs quoted, but you can definitely go quite a bit higher if you only want a small amount of data as output).

Have you tried splitting your data into two (or more) smaller chunks?

Emily

Answer 2

[Sudeep]

Have you tried using refseq to uniprot mappings that are available from NCBI itself ? refseq to uniprot mappings are available in this file

[prajwalnj]

Thank you, but these are just for the protein ids, is there a similar file for the nucleotide ids (mRNA) as well ?

Answer 3

[Assa Yeroslaviz]

What about the uniprot site?

They have an ID mapping tab, where you can convert a lot of different ID to other IDs.

Assa