Pombe Intron Locations
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9.7 years ago
Varun Gupta ★ 1.2k

Hi Everyone

So i am interested in finding only the intron start and intron ends for list of genes i have for S.pombe genome.

I came across ensembl and here is the link i am attaching

As you scroll down you will see intron and its start and end coordinates.

I need to extract these intronic coordinates only for a list of my genes.

How can i do it from ensembl.

Any code would be really appreciated. I am new to this kind of thing

Hope to hear from you soon

Regards

intron coordinates • 2.6k views
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9.7 years ago
Ahdf-Lell-Kocks ★ 1.6k

Install the fungi API as instructed here:
http://fungi.ensembl.org/info/docs/api/api_installation.html

You can modify the script to give you the start and end coordinates, and do that only for the list of genes you are interested in:

use strict;
use warnings;

use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Utils::SeqDumper;

my $registry = 'Bio::EnsEMBL::Registry'; # For EnsemblGenomes$registry->load_registry_from_db(
-host => 'mysql.ebi.ac.uk',
-port => 4157,
-user => 'anonymous',
#    -verbose => 1
);

# For Ensembl
# $registry->load_registry_from_db( '-host' => 'ensembldb.ensembl.org', # '-port' => '5306', # '-user' => 'anonymous', # '-db_version' => '65' ); my @list = ('SPAC24H6.01c','SPAC2F7.03c','SPAC2F7.04c','SPAC2F7.05c'); my$ga = $registry->get_adaptor( 'schizosaccharomyces_pombe', 'Core', 'Gene' ); my$dumper = Bio::EnsEMBL::Utils::SeqDumper->new();

foreach my $id (@list) { my$gene = $ga->fetch_by_stable_id($id);
next unless (defined $gene); foreach my$transcript (@{ $gene->get_all_Transcripts } ) { next unless (defined$transcript);
foreach my $intron ( @{$transcript->get_all_Introns() } ) {
next unless (defined $intron); print$intron->feature_Slice->display_id,"\n";
# $dumper->dump($intron->feature_Slice(), 'FASTA' );
}
}
}

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hi i tried the code and it said that schizosaccharomyces_pombe is not a valid species name can you tell me what can be the problem

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Did you download the API from fungi.ensembl.org? Added comment on top.