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Can not download gi_list from NCBI

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?

rna-seq
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written by felix.kuo.1211 1

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

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written by piet 185

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

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written by Tonor 48

2 answers

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/.

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written by mastal511 211

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

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written by felix.kuo.1211 1

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.

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written by Tonor 48

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

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written by Tonor 48

I need all bactieria's GI number.

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written by felix.kuo.1211 1

It seems to work for nucleotides, but not proteins

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written by Tonor 48

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

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written by felix.kuo.1211 1

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