Pombe Intron Locations

Question

[Varun Gupta]

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

link text

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

[Casey Bergman]

Follow-on question from: http://biostar.stackexchange.com/questions/17683/s-pombe-intron-coordinates

Answer 1

[Ahdf-Lell-Kocks]

From this answer in a previous post

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' );
        }
    }
}

[Varun Gupta]

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

[2184687-1231-83-]

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