Getting GI number from NCBI database through code

Question

[erans995]

Hello As part of a college project, I have to write a program that finds similar FASTA sequences to a one the user chooses. In my program, say the user enters "cat", I have to display to him all the relevant entries present in the DB, and let him choose one. I have a script that outputs the FASTA data of a certain entry in the NCBI database given its accession number.

I have found the following perl script that converts GI to accession number:

use LWP::Simple;
$gi_list = '24475906,224465210,50978625,9507198';

#assemble the URL
$base = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/';
$url = $base . "efetch.fcgi?db=nucleotide&id=$gi_list&rettype=acc";

#post the URL
$output = get($url);
print "$output";

However, I haven't found a way to retrieve the GI from the database through code. Thank you for taking the time to read this, I hope you will be able to help me!

[Chris Fields]

I normally don't post replies to homework or project-based questions, but I'll simply point to this post (and indicate you should point this out to your course instructor, it's been two years since the original announcement):

https://www.ncbi.nlm.nih.gov/books/NBK431010/#news_03-02-2016-phase-out-of-GI-numbers

[erans995]

Okay thanks for the update. Let me rephrase my question: how can I retrieve the accession number of a certain entry through code?

[GenoMax]

See my answer below.

Answer 1

[GenoMax]

NCBI deprecated use of GI numbers in 2016. You should switch your code to using Accession numbers.

NCBI Unix utils allow you to query using gi and retrieve accessions numbers.

$ esearch -db nuccore -query "24475906" | efetch -format acc
NM_009417.2

[erans995]

But that's the point, how can I retrieve the GI through code? I don't know it...

[GenoMax]

I thought you already had gi numbers. Using your "cat" example you can get accession numbers like this.

$ esearch -db nuccore -query "cat" | efetch -format acc

AFHV02000288.1
AFHV02000289.1
AFHV02000291.1
AFHV02000292.1
AFHV02000293.1
AFHV02000294.1

I will leave it to you to figure out how to change the query and how to use this method to do URL based searches.

[erans995]

Okay thank you very much, I'll try to figure out the rest by myself