This is a test version of Biostars. For the public version, visit https://www.biostars.org.
News: NCBI is going to eliminate GI identifiers

NCBI gets rid of the old GI identifiers for sequence records by September 2016, see here.

ncbi gi
• 3,735 views • link
updated by Ram Ram • written by Anima Mundi Anima Mundi

would all existing entries change or only the new submissions?

• 0 views • link
written by Naren Naren

Appears to be all entries. GI's may still be used internally at NCBI but they will not be visible/included in GenBank, GenPept, and FASTA records.

• 0 views • link
written by GenoMax GenoMax

Indeed, as far as I understood is going to be eliminated from all entries.

• 0 views • link
written by Anima Mundi Anima Mundi

Although they now provide accession2taxid map files, these do not work with makeblastdb -taxid_map option even if you parse columns 2 and 3 (accession.version & taxid) into their own file. It's relatively painless to join the taxids to tabular blast output, but it gets less convenient if you also want to see e.g. "sscinames" ;-( There should really be taxid2alltaxinfo map files..

• 0 views • link
written by 5heikki 5heikki

I suggest that you send that request in to BLAST help email address. Perhaps NCBI will start making that file available by the time GI gets phased out in September 2016.

• 0 views • link
written by GenoMax GenoMax

I did that yesterday. At least right now there is no solution and you have to do post processing yourself.

• 0 views • link
written by 5heikki 5heikki

This. It's crazy how many slow API alls are required to extract meaningful taxonomic information from BLAST results. It's hilariously user unfriendly. Thanks for making the request.

• 0 views • link
written by bedeabc bedeabc

So it looks like we'll soon have to do this to get any meangful info from BLAST results:

  • GI -> accession.version
  • accession.version > taxid
  • taxid > taxonomy

Someone please tell me there's a better solution

• 0 views • link
written by bedeabc bedeabc

0 answers

No answers yet.

Log in to answer this question.

More posts like this