Can not download gi_list from NCBI

Question

[felix.kuo.1211]

I have go to https://www.ncbi.nlm.nih.gov/protein/?term=txid2%5BORGN%5D+

And use Send to>File>gi list.

But I got "sequence.gi" and it is null. (0KB)

How can I download it?

[piet]

you are searching for the term "taxid2[ORGN]" which is nonsense. Try to replace "taxid2" by a valid taxon name.

[Tonor]

Yeah - your query returns 273195473 results! suspect that may have something to do it. As piet suggests, if you narrowed it down to a specific taxon, say just zika viruses it seems to work: https://www.ncbi.nlm.nih.gov/protein/?term=txid64320%5BOrganism%3Anoexp%5D

But as mastal511 metions below, as GIs have been discontinued, best to move on from them, and rely on accession numbers

Answer 1

[mastal511]

It might be because NCBI has decided to discontinue use of GI numbers.

See https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/.

Answer 2

[felix.kuo.1211]

Use Send to>File>accession numbers I got a same ans.

[Tonor]

What are you trying to download? Your query returns 273195473 results - is that what you really want? If so you are better off going to genbank ftp site and getting data direct from there.

[felix.kuo.1211]

I find an old nr at ftp://genesilico.pl/lukaskoz/biological_databases/. And it is gi format.

I want to use Vertebrate Subset Nr Database? Build My Own? to make a nr bacteria subset.

[Tonor]

As piet says above - you current query is using taxid2 -> what taxid are you wanting? txid7742[ORGN] is what was used in the blog post you mentioned

[felix.kuo.1211]

I need all bactieria's GI number.

[Tonor]

It seems to work for nucleotides, but not proteins

[felix.kuo.1211]

It is said that BLASTx can mapping RNA to nr database. But nr is to big. I want to make a subset nr.