NCBI Protein GI to Genome Accession
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4
Entering edit mode
7.2 years ago
Sej Modha 5.1k

I have a list of protein GI and would like to get accession number of the genome (DBSOURCE in genbank file) using Eutilities.

What would be the easiest way to get genome accession numbers for a list of protein GI?

sequence eutils ncbi • 7.4k views
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6
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6.3 years ago
Sej Modha 5.1k

An alternative to perl e-util is to use the Unix e-utils. Following one liner does the job! Note that following command would work for accession number as well as GIs as -id parameter in elink command.

elink -db protein -id 817524604 -target nuccore|efetch -format acc
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5
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7.2 years ago
GenoMax 119k

For future reference:

There is an interesting file @NCBI which contains information about various accession numbers/gene names: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz

This file is automatically generated everyday and should contain latest information about GeneID's and accession numbers.

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Just wanted to say thanks for this, this saved me a massive amount of time genomax2!

I threw together a makefile and a small python script to convert the 4.8Gb uncompressed file into a kyoto-cabinet database in case anyone wants it.

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4
Entering edit mode
7.2 years ago
Sej Modha 5.1k

Here is a perl script to do this. This script is explained in detail here

#!/usr/bin/perl

use Bio::DB::EUtilities;

#my @ids     = qw(817524604 726965494);
my $infile = $ARGV[0];
my @ids;

open (IN,"$infile")||die "can't open $infile\n";

while(<IN>)
{
  chomp($_);
  my @ids=$_;
# print @ids."\n";    
  my $factory = Bio::DB::EUtilities->new(-eutil          => 'elink',
                                       -email          => 'mymail@foo.bar',
                                       -db             => 'nucleotide',
                                       -dbfrom         => 'protein',
                                       -correspondence => 1,
                                       -id             => \@ids);

  # iterate through the LinkSet objects
  while (my $ds = $factory->next_LinkSet) 
  {
    #print "   Link name: ",$ds->get_link_name,"\n";
    my $protid = join(',',$ds->get_submitted_ids);
    print "Protein ID:" . $protid ."\t";
    #print "Protein ID: ",join(',',$ds->get_submitted_ids),"\t";
    my $nucid = join(',',$ds->get_ids);
    print "Nuc ID:" . $nucid ."\t";
    my $factory = Bio::DB::EUtilities->new(-eutil   => 'efetch',
                           -db      => 'nucleotide',
                                              -id      => $nucid,
                                              -email   => 'mymail@foo.bar',
                                              -rettype => 'acc');
   my @accs = split(m{\n},$factory->get_Response->content);
   print "Genome Accession: " .join(',',@accs), "\n";
   }
}
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0
Entering edit mode
2.3 years ago
josev.die ▴ 50

Using #R :

# Dependencies
library(rentrez) 

# NCBI Protein GI to Genome Accession
gi = 817524604
gi_link = entrez_link(dbfrom = 'protein', db = 'nuccore', id = gi)
nucc_id = gi_link$links$protein_nuccore
nucc = entrez_summary(db = 'nuccore', id = nucc_id)
nucc$caption
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