<p>Hi,</p>

<p>I would like to know how could I download all the introns (in FASTA) of a species from Ensembl via web.</p>

<p>Hi,</p>

<p>As far as I know, we don't store the intron sequences explicitly anywhere.</p>

<p>Here's a piece of Perl code that uses the Ensembl Perl API to fetch all intron sequences for the transcripts overlapping a particular region on the first human chromosome. It can easily be modified to fetch all transcripts in the species and to dump the sequence to a file instead of to the screen:</p>

<pre><code>use strict;
use warnings;

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

my $registry = 'Bio::EnsEMBL::Registry';

$registry-&gt;load_registry_from_db( '-host' =&gt; 'ensembldb.ensembl.org',
                                  '-port' =&gt; '5306',
                                  '-user' =&gt; 'anonymous',
                                  '-db_version' =&gt; '63' );

my $sa = $registry-&gt;get_adaptor( 'Human', 'Core', 'Slice' );
my $slice = $sa-&gt;fetch_by_region( 'Chromosome', '1', 12_000, 13_000 );

my $dumper = Bio::EnsEMBL::Utils::SeqDumper-&gt;new();

foreach my $transcript ( @{ $slice-&gt;get_all_Transcripts() } ) {
  foreach my $intron ( @{ $transcript-&gt;get_all_Introns() } ) {
    $dumper-&gt;dump( $intron-&gt;feature_Slice(), 'FASTA' );
  }
}
</code></pre>

<p>I hope this helps.</p>
