By "uniprot ids" do you mean UniProtKB entry names (e.g. BRCA1_HUMAN) or accessions (e.g. P38398)?
Since UniProtKB entry names are subject to change, you may need to map any entry names you are using to accessions before attempting to perform further mappings.
Also do you mean Entrez Gene identifiers or NCBI GI numbers?
If the former, then:
If you want GI numbers then you can do much the same thing, but instead of querying Entrez Gene you need to query the 'Protein' database (which includes all the sequence data in UniProtKB), and will return the NCBI version of the UniProtKB entry, including the GI number assigned to the current protein sequence.
You could also try mapping your UniProtKB accessions (or entry names) through UniParc to RefSeq. Since this mapping is based on sequence identity, instead of the UniProtKB cross-reference annotations (which do not exist for some organisms), it will give you RefSeq entries which have the same sequence. You can then look-up these RefSeq identifiers in Entrez Gene to get the best coverage possible for a set of sequence entries. It may be possible to go further by including older sequence versions in the mapping, however these are typically updated to correct sequencing errors, and so should be treated with caution.
modified 6.2 years ago
6.2 years ago by
Hamish • 3.1k