[ensembl-dev] GRCh37 Protein sequence has asterisks

Luke Goodsell l.goodsell at achillestx.com
Mon Dec 4 15:57:33 GMT 2017


I’ve been trying to retrieve some GRCh37 protein sequences with code similar to that below and have found some proteins that have corrupted sequences, including asterisks. Please can you tell me how to get the correct protein sequences?

#!/usr/bin/env perl

use strict;

use warnings;

use Bio::EnsEMBL::Registry;

use Getopt::Long qw(GetOptionsFromArray);

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


    -host => 'ensembldb.ensembl.org',

    -user => 'anonymous',

    -port => '3337'


my $transcript_adaptor = $registry->get_adaptor( 'Human', 'otherfeatures', 'Transcript' );

foreach my $transcript_id ("NM_002426.4") {

    foreach my $transcript (@{ $transcript_adaptor->fetch_all_versions_by_stable_id($transcript_id) }) {

        my $protein = $transcript->translation();

        defined($protein) or next;

        print ">" . $protein->stable_id() . "\n";

        print $protein->seq() . "\n";



Kind regards,
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