protein databases with GI numbers

Question

[yp19]

Hi all,

Anyone know whether NCBI (or any other website) has a protein database that includes GI numbers for each protein? I have read that they have become obsolete in the NCBI nr database as of a few years ago, and when I blastp against the nr database I do not see them as part of the output.

Thanks!

[GenoMax]

While gi numbers are in use internally at NCBI you should not plan on using them for any purpose. Accession numbers is what the new standard is.

[yp19]

Yes that is true, however I'm trying to run a tool that requires gi numbers as part of the input (Horizontal gene transfer tool) Is there anyway around this?

[GenoMax]

If you must get gi then you could try to retrieve them using Entrezdirect. Here is an example of how you would do this.

$ esearch -db protein -query "CAA62188.1" | efetch -format gi
1212992

Answer 1

[Elisabeth Gasteiger]

If you have UniProtKB identifiers for your proteins, you can try the UniProt IDmapping tool at https://www.uniprot.org/uploadlists to map from UniProt to GI numbers. However, the underlying data is based on the GI numbers that existed before NCBI obsoleted them, and the tool may therefore not be able to map all your proteins.