Hi Perlmonks,

I am interested in retrieving the transcript, 5 prime and 3 prime UTR of an Ensembl transcript identifier like ENST00000528762. I have searched in the web and have not found any script for auto downloading the desired sequences. Then I have tried with the following script. The script does not work and gives the cmd output indicating some problems in driver. I could not sort out the problem. Is it possible to retrieve the transcript in fasta format along with 5 prime and 3 prime UTR sequences of the transcript using any other perl code? I welcome suggestions from perlmonks.

Here goes the code x3.pl 

 #!/usr/bin/perl
use warnings; 
use strict; 

 use Bio::EnsEMBL::Registry;

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

 $registry->load_registry_from_db(
    -host => 'useastdb.ensembl.org', # alternatively 'useastdb.ensembl
+.org'
    -user => 'anonymous');  

 my $stable_id = 'ENST00000528762';

 my $transcript_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Tr
+anscript' );
 my $transcript = $transcript_adaptor->fetch_by_stable_id($stable_id);

print "\n Transcript: $transcript\n"; 

# UTR sequences are obtained via the five_prime_utr() and
# three_prime_utr() methods:

 my $fiv_utr = $transcript->five_prime_utr('ENST00000528762');
 my $thr_utr = $transcript->three_prime_utr('ENST00000528762');

print "\n 5' UTR: ", ( defined $fiv_utr ? $fiv_utr->seq() : "None" ), 
+"\n";
print "\n 3' UTR: ", ( defined $thr_utr ? $thr_utr->seq() : "None" ), 
+"\n";

exit;

[download]

I have got the output in cmd as follows: 

 C:\Users\x>cd d*

C:\Users\x\Desktop>x3.pl
install_driver(mysql) failed: Can't locate Mysql/Statement.pm in @INC 
+(@INC cont
ains: C:/Perl/site/lib C:/Perl/lib .) at C:/Perl/lib/DBD/mysql.pm line
+ 12.
Compilation failed in require at (eval 12) line 3.
Perhaps a module that DBD::mysql requires hasn't been fully installed
 at C:/Perl/lib/Bio/EnsEMBL/Registry.pm line 1765.

C:\Users\x\Desktop>

[download]

In reply to How can one retrieve the transcript, 5 prime and 3 prime UTR of an Ensembl identifier? by supriyoch_2008

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