Modifying Genbank File To Visualize Genes Using Artemis

Question

[Carol]

Hi all, I'm trying to visualize certain genes using sanger's genome visualization tool Artemis.For that I want to modify a Genbank file by adding misc_features and their value as the sequnece start..end and /colour=2 identifier between FEATURES and SOURCE identifiers as follows:

FEATURES             Location/Qualifiers
     misc_feature     3360096..3361436
                      /colour=2
     misc_feature     2931510..2932826
                      /colour=2
     misc_feature     904348..906762
                      /colour=2
source          1..3544776
                     /organism="Geobacillus kaustophilus HTA426"
                     /mol_type="genomic DNA"
                     /strain="HTA426"
                     /isolation_source="isolated from the deepest Ocean"
                     /db_xref="taxon:235909"
                     /note="thermophile"

As this is going to be implemented with a lot of genes and genomes therefore could anybody suggest me a perl script which does this job by taking sequence coordinate(start..end) and the genbank file (to be modified) as input and outputing the desired Genbank file.Any help is highly appreciated.

Answer 1

[Neilfws]

Take a look at the Bioperl Feature Annotation HOW-TO, in particular the section Building Your Own Sequences. It should make your task very easy.

Briefly, you read in the GenBank file like this:

use strict;
use Bio::SeqIO;

my $seqio = Bio::SeqIO->new(-file => "myfile.gb", -format => "genbank");
my $gb    = $seqio->next_seq;

Then you can create your feature like this (assuming you can get start/end from somewhere):

use Bio::SeqFeature::Generic;
my $feat = Bio::SeqFeature::Generic->new(-start       => 3360096,
                                         -end         => 3361436,
                                         -primary_tag => 'misc_feature',
                                         -tag         => {colour => "2"});

Add it to the sequence object:

$gb->add_SeqFeature($feat);

And write out a new GenBank file:

my $outseq = Bio::SeqIO->new(-format => "genbank", -file => ">mynewfile.gb" );
$outseq->write_seq($gb);