Programming Language: Perl
Modules required: Bio::DB::EUtilities

EUtilities is a very useful resource to retrieve data from NCBI database.

This script retrieves a brief summary and the genbank file for genes that are relevant to a search word.

There is also an option to limit you number of results returns (very handy).

Bio::DB::EUtilities is required to execute the search.

This method is much faster than using Bio::DB::Query::GenBank module.

If you require more information than the summary output, you can always get it from the genbank file.
The summary does not provide information such as references and sequences.

Chapter 10 of ‘Beginning Perl for Bioinformatics’ is a good and simple reference for retrieving data from from files in genbank format. This resource is freely available here.

Note that you can query for proteins as well. (uncomment line 15)

Installing new modules: this can be easily done using cpan.
Here is the documentation for cpan.
Or, here is documentation for installing modules manually.

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#!/usr/bin/perl -w
 
use Bio::DB::EUtilities; 
use strict;
 
#specify search term 
my $search_term = 'breast cancer';			
 
 
#maximum number of results to retrieve
my $retmax = 10;
 
#first search for a list of genbank ids that match your search term
my $factory = Bio::DB::EUtilities->new(-eutil => 'esearch',
#                           -db => 'protein',
                         -db => 'nucleotide',
                         -term => $search_term,
                         -retmax => $retmax);
 
#list of Genbank IDs
my @ids = $factory->get_ids;
 
#loop through the list of IDs
foreach my $id (@ids){
 
	# get a summary and print details
		$factory->reset_parameters(-eutil => 'esummary',-db => 'nucleotide',-id => $id); 
		my $ds = $factory->next_DocSum; 
 
		# print flattened mode from summary above 
		while (my $item = $ds->next_Item('flattened'))  { 
			# checks id itens has contents
			printf("%-20s:%s\n",$item->get_name,$item->get_content) if $item->get_content; 
		} 
 
 
	# download the full genbank file 
		$factory = Bio::DB::EUtilities->new(-eutil => 'efetch', 
								-db => 'nucleotide', 
								-id => $id, 
								-rettype => 'gbwithparts'); 								
		$factory->get_Response(-file => "$id.gb"); 
 
}