How to get enome feature annotation through NCBI api ?

Question

[demolidd77]

Hi,

I wanna get the whole genome annotion result with some information ,like transcript,exon,gene etc , As we know ,NCBI has provided the GFF file containing the above information , but I wanna get the latest content from NCBI online website because the website is latest, no delay! . so where can I find NCBI API to download gene annotation batchly ?

Thanks!

[Luis Nassar]

You can also query NCBI's data from UCSC's API (https://genome.ucsc.edu/goldenPath/help/api.html) in the following fashion:

https://api.genome.ucsc.edu/getData/track?genome=hg38;track=ncbiRefSeq;maxItemsOutput=100

Although better to query the original source when possible.

Answer 1

[Carambakaracho]

NCBI eutils: https://www.ncbi.nlm.nih.gov/books/NBK25500/

see also command line alternative edirect https://www.ncbi.nlm.nih.gov/books/NBK179288/

[demolidd77]

Hello, @Carambakaracho

Do you know which command or API can return GFF contents like this format ?

NC_000001.10 RefSeq region 1 249250621 . + . ID=NC_000001.10:1..249250621;Dbxref=taxon:9606;

if I only have every chromosome location range ,like chr1:1-1345673, is there any API command to support with returning like above GFF format contents ?

Thanks !

[Carambakaracho]

My apology, I'm a bit rusty using these commands, they're not in the focus of my job anymore.

[demolidd77]

Thank you anyway ! !!!