supriyoch_2008 has asked for the wisdom of the Perl Monks concerning the following question:

I am interested in retrieving a DNA sequence from the GenBank database of NCBI using a perl program run in my perl 5.10 version. I searched for such perl scripts online and came across the following code (given below) as ocs5.pl. When I tried to run the code in command prompt, the perl script produced several warnings (given below). Then I tried to resolve the issue of “500 SSL negotiation failed “ after reading a few online posts. As per the online suggestions, I updated LWP::Protocol::https, IO::Socket::SSL, Net::SSLeay, OpenSSL and Bio modules from cpan (https://www.cpan.org/) inside the lib folder of Perl. The problem still persists. I seek the advice of the perl monks/experts to fix this problem.

Here goes the ocs5.pl code: 

 
#!/usr/bin/perl 
use strict;
use warnings;
use Bio::DB::GenBank;
# Create a new GenBank database object
my $db = Bio::DB::GenBank->new;
# Desired GenBank accession number
my $accession = 'NM_000059.4'; 
# Retrieve the sequence object
my $seq = $db->get_Seq_by_acc($accession);
# Print the sequence display ID
if ($seq) {
    print "\n Sequence ID: ", $seq->display_id, "\n";
    # You can access other information like the sequence itself:
     print "\n Sequence: ", $seq->seq, "\n";
    # To save the sequence to a FASTA file:
     use Bio::SeqIO;
     my $seq_out = Bio::SeqIO->new(-file => ">your_sequence.fasta", -f
+ormat => 'fasta');
     $seq_out->write_seq($seq);
} else {
    print "\n Could not retrieve sequence for accession: $accession\n"
+; } 
exit;

[download]

I get the following warnings after running the code: 

 Microsoft Windows [Version 10.0.22631.5472]
(c) Microsoft Corporation. All rights reserved.
C:\Users\srinj>cd desktop
C:\Users\srinj\Desktop>ocs5.pl
------------- EXCEPTION -------------
MSG: WebDBSeqI Request Error:
500 SSL negotiation failed:
Content-Type: text/plain
Client-Date: Fri, 25 Jul 2025 04:21:08 GMT
Client-Warning: Internal response
500 SSL negotiation failed:
STACK Bio::DB::WebDBSeqI::_request C:/Perl/lib/Bio/DB/WebDBSeqI.pm:708
STACK Bio::DB::WebDBSeqI::get_seq_stream C:/Perl/lib/Bio/DB/WebDBSeqI.
+pm:514
STACK Bio::DB::NCBIHelper::get_Stream_by_acc C:/Perl/lib/Bio/DB/NCBIHe
+lper.pm:502
STACK Bio::DB::WebDBSeqI::get_Seq_by_acc C:/Perl/lib/Bio/DB/WebDBSeqI.
+pm:194
STACK toplevel C:\Users\srinj\Desktop\ocs5.pl:15
-------------------------------------

[download]

The expected output should look as follows: 

 >NM_000059.4 Homo sapiens BRCA2 DNA repair associated (BRCA2), transc
+ript variant 1, mRNA
AGAGGCGGAGCCGCTGTGGCACTGCTGCGCCTCTGCTGCGCCTCGGGTGTCTTTTGCGGCGGTGGGTCGC
CGCCGGGAGAAGCGTGAGGGGACAGATTTGTGACCGGCGCGGTTTTTGTCAGCTTACTCCGGCCAAAAAA
GAACTGCACCTCTGGAGCGGACTTATTTACCAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGG
ATCCAAAGAGAGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGATTTAGGACCAATA
AGTCTTAATTGGTTTGAAGAACTTTCTTCAGAAGCTCCACCCTATAATTCTGAACCTGCAGAAGAATCTG
AACATAAAAACAACAATTACGAACCAAACCTATTTAAAACTCCACAAAGGAAACCATCTTATAATCAGCT
GGCTTCAACTCCAATAATATTCAAAGAGCAAGGGCTGACTCTGCCGCTGTACCAATCTCCTGTAAAAGAA
TTAGATAAATTCAAATTAGACTTAGGAAGGAATGTTCCCAATAGTAGACATAAAAGTCTTCGCACAGTGA
AAACTAAAATGGATCAAGCAGATGATGTTTCCTGTCCACTTCTAAATTCTTGTCTTAGTGAAAGTCCTGT
TGTTCTACAATGTACACATGTAACACCACAAAGAGATAAGTCAGTGGTATGTGGGAGTTTGTTTCATACA
CCAAAGTTTGTGAAGGGTCGTCAGACACCAAAACATATTTCTGAAAGTCTAGGAGCTGAGGTGGATCCTG
ATATGTCTTGGTCAAGTTCTTTAGCTACACCACCCACCCTTAGTTCTACTGTGCTCATAGTCAGAAATGA
AGAAGCATCTGAAACTGTATTTCCTCATGATACTACTGCTAATGTGAAAAGCTATTTTTCCAATCATGAT
GAAAGTCTGAAGAAAAATGATAGATTTATCGCTTCTGTGACAGACAGTGAAAACACAAATCAAAGAGAAG
CTGCAAGTCATGGATTTGGAAAAACATCAGGGAATTCATTTAAAGTAAATAGCTGCAAAGACCACATTGG
AAAGTCAATGCCAAATGTCCTAGAAGATGAAGTATATGAAACAGTTGTAGATACCTCTGAAGAAGATAGT
TTTTCATTATGTTTTTCTAAATGTAGAACAAAAAATCTACAAAAAGTAAGAACTAGCAAGACTAGGAAAA
AAATTTTCCATGAAGCAAACGCTGATGAATGTGAAAAATCTAAAAACCAAGTGAAAGAAAAATACTCATT
TGTATCTGAAGTGGAACCAAATGATACTGATCCATTAGATTCAAATGTAGCAAATCAGAAGCCCTTTGAG
AGTGGAAGTGACAAAATCTCCAAGGAAGTTGTACCGTCTTTGGCCTGTGAATGGTCTCAACTAACCCTTT
CAGGTCTAAATGGAGCCCAGATGGAGAAAATACCCCTATTGCATATTTCTTCATGTGACCAAAATATTTC
AGAAAAAGACCTATTAGACACAGAGAACAAAAGAAAGAAAGATTTTCTTACTTCAGAGAATTCTTTGCCA
CGTATTTCTAGCCTACCAAAATCAGAGAAGCCATTAAATGAGGAAACAGTGGTAAATAAGAGAGATGAAG
AGCAGCATCTTGAATCTCATACAGACTGCATTCTTGCAGTAAAGCAGGCAATATCTGGAACTTCTCCAGT
GGCTTCTTCATTTCAGGGTATCAAAAAGTCTATATTCAGAATAAGAGAATCACCTAAAGAGACTTTCAAT
GCAAGTTTTTCAGGTCATATGACTGATCCAAACTTTAAAAAAGAAACTGAAGCCTCTGAAAGTGGACTGG
AAATACATACTGTTTGCTCACAGAAGGAGGACTCCTTATGTCCAAATTTAATTGATAATGGAAGCTGGCC
AGCCACCACCACACAGAATTCTGTAGCTTTGAAGAATGCAGGTTTAATATCCACTTTGAAAAAGAAAACA
AATAAGTTTATTTATGCTATACATGATGAAACATCTTATAAAGGAAAAAAAATACCGAAAGACCAAAAAT
CAGAACTAATTAACTGTTCAGCCCAGTTTGAAGCAAATGCTTTTGAAGCACCACTTACATTTGCAAATGC
TGATTCAGGTTTATTGCATTCTTCTGTGAAAAGAAGCTGTTCACAGAATGATTCTGAAGAACCAACTTTG
TCCTTAACTAGCTCTTTTGGGACAATTCTGAGGAAATGTTCTAGAAATGAAACATGTTCTAATAATACAG
TAATCTCTCAGGATCTTGATTATAAAGAAGCAAAATGTAATAAGGAAAAACTACAGTTATTTATTACCCC
AGAAGCTGATTCTCTGTCATGCCTGCAGGAAGGACAGTGTGAAAATGATCCAAAAAGCAAAAAAGTTTCA
GATATAAAAGAAGAGGTCTTGGCTGCAGCATGTCACCCAGTACAACATTCAAAAGTGGAATACAGTGATA
CTGACTTTCAATCCCAGAAAAGTCTTTTATATGATCATGAAAATGCCAGCACTCTTATTTTAACTCCTAC
TTCCAAGGATGTTCTGTCAAACCTAGTCATGATTTCTAGAGGCAAAGAATCATACAAAATGTCAGACAAG
CTCAAAGGTAACAATTATGAATCTGATGTTGAATTAACCAAAAATATTCCCATGGAAAAGAATCAAGATG
TATGTGCTTTAAATGAAAATTATAAAAACGTTGAGCTGTTGCCACCTGAAAAATACATGAGAGTAGCATC
ACCTTCAAGAAAGGTACAATTCAACCAAAACACAAATCTAAGAGTAATCCAAAAAAATCAAGAAGAAACT
ACTTCAATTTCAAAAATAACTGTCAATCCAGACTCTGAAGAACTTTTCTCAGACAATGAGAATAATTTTG
TCTTCCAAGTAGCTAATGAAAGGAATAATCTTGCTTTAGGAAATACTAAGGAACTTCATGAAACAGACTT
GACTTGTGTAAACGAACCCATTTTCAAGAACTCTACCATGGTTTTATATGGAGACACAGGTGATAAACAA
GCAACCCAAGTGTCAATTAAAAAAGATTTGGTTTATGTTCTTGCAGAGGAGAACAAAAATAGTGTAAAGC
AGCATATAAAAATGACTCTAGGTCAAGATTTAAAATCGGACATCTCCTTGAATATAGATAAAATACCAGA
AAAAAATAATGATTACATGAACAAATGGGCAGGACTCTTAGGTCCAATTTCAAATCACAGTTTTGGAGGT
AGCTTCAGAACAGCTTCAAATAAGGAAATCAAGCTCTCTGAACATAACATTAAGAAGAGCAAAATGTTCT
TCAAAGATATTGAAGAACAATATCCTACTAGTTTAGCTTGTGTTGAAATTGTAAATACCTTGGCATTAGA
TAATCAAAAGAAACTGAGCAAGCCTCAGTCAATTAATACTGTATCTGCACATTTACAGAGTAGTGTAGTT
GTTTCTGATTGTAAAAATAGTCATATAACCCCTCAGATGTTATTTTCCAAGCAGGATTTTAATTCAAACC
ATAATTTAACACCTAGCCAAAAGGCAGAAATTACAGAACTTTCTACTATATTAGAAGAATCAGGAAGTCA
GTTTGAATTTACTCAGTTTAGAAAACCAAGCTACATATTGCAGAAGAGTACATTTGAAGTGCCTGAAAAC
CAGATGACTATCTTAAAGACCACTTCTGAGGAATGCAGAGATGCTGATCTTCATGTCATAATGAATGCCC
CATCGATTGGTCAGGTAGACAGCAGCAAGCAATTTGAAGGTACAGTTGAAATTAAACGGAAGTTTGCTGG
CCTGTTGAAAAATGACTGTAACAAAAGTGCTTCTGGTTATTTAACAGATGAAAATGAAGTGGGGTTTAGG
GGCTTTTATTCTGCTCATGGCACAAAACTGAATGTTTCTACTGAAGCTCTGCAAAAAGCTGTGAAACTGT
TTAGTGATATTGAGAATATTAGTGAGGAAACTTCTGCAGAGGTACATCCAATAAGTTTATCTTCAAGTAA
ATGTCATGATTCTGTTGTTTCAATGTTTAAGATAGAAAATCATAATGATAAAACTGTAAGTGAAAAAAAT
AATAAATGCCAACTGATATTACAAAATAATATTGAAATGACTACTGGCACTTTTGTTGAAGAAATTACTG
AAAATTACAAGAGAAATACTGAAAATGAAGATAACAAATATACTGCTGCCAGTAGAAATTCTCATAACTT
AGAATTTGATGGCAGTGATTCAAGTAAAAATGATACTGTTTGTATTCATAAAGATGAAACGGACTTGCTA
TTTACTGATCAGCACAACATATGTCTTAAATTATCTGGCCAGTTTATGAAGGAGGGAAACACTCAGATTA
AAGAAGATTTGTCAGATTTAACTTTTTTGGAAGTTGCGAAAGCTCAAGAAGCATGTCATGGTAATACTTC
AAATAAAGAACAGTTAACTGCTACTAAAACGGAGCAAAATATAAAAGATTTTGAGACTTCTGATACATTT
TTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTGTAAATTTCTTTG
ATCAGAAACCAGAAGAATTGCATAACTTTTCCTTAAATTCTGAATTACATTCTGACATAAGAAAGAACAA
AATGGACATTCTAAGTTATGAGGAAACAGACATAGTTAAACACAAAATACTGAAAGAAAGTGTCCCAGTT
GGTACTGGAAATCAACTAGTGACCTTCCAGGGACAACCCGAACGTGATGAAAAGATCAAAGAACCTACTC
TATTGGGTTTTCATACAGCTAGCGGGAAAAAAGTTAAAATTGCAAAGGAATCTTTGGACAAAGTGAAAAA
CCTTTTTGATGAAAAAGAGCAAGGTACTAGTGAAATCACCAGTTTTAGCCATCAATGGGCAAAGACCCTA
AAGTACAGAGAGGCCTGTAAAGACCTTGAATTAGCATGTGAGACCATTGAGATCACAGCTGCCCCAAAGT
GTAAAGAAATGCAGAATTCTCTCAATAATGATAAAAACCTTGTTTCTATTGAGACTGTGGTGCCACCTAA
GCTCTTAAGTGATAATTTATGTAGACAAACTGAAAATCTCAAAACATCAAAAAGTATCTTTTTGAAAGTT
AAAGTACATGAAAATGTAGAAAAAGAAACAGCAAAAAGTCCTGCAACTTGTTACACAAATCAGTCCCCTT
ATTCAGTCATTGAAAATTCAGCCTTAGCTTTTTACACAAGTTGTAGTAGAAAAACTTCTGTGAGTCAGAC
TTCATTACTTGAAGCAAAAAAATGGCTTAGAGAAGGAATATTTGATGGTCAACCAGAAAGAATAAATACT
GCAGATTATGTAGGAAATTATTTGTATGAAAATAATTCAAACAGTACTATAGCTGAAAATGACAAAAATC
ATCTCTCCGAAAAACAAGATACTTATTTAAGTAACAGTAGCATGTCTAACAGCTATTCCTACCATTCTGA
TGAGGTATATAATGATTCAGGATATCTCTCAAAAAATAAACTTGATTCTGGTATTGAGCCAGTATTGAAG
AATGTTGAAGATCAAAAAAACACTAGTTTTTCCAAAGTAATATCCAATGTAAAAGATGCAAATGCATACC
CACAAACTGTAAATGAAGATATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAA
TGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCC
AGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCA
GTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAAATTTGCCAAACGAAAATTATGGCAGGTTGTTA
CGAGGCATTGGATGATTCAGAGGATATTCTTCATAACTCTCTAGATAATGATGAATGTAGCACGCATTCA
CATAAGGTTTTTGCTGACATTCAGAGTGAAGAAATTTTACAACATAACCAAAATATGTCTGGATTGGAGA
AAGTTTCTAAAATATCACCTTGTGATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAA
GCTTCATAAGTCAGTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAG
GTATCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCT
TTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACG
TACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGA
TTTAGTACAGCAAGTGGAAAGCAAGTTTCCATTTTAGAAAGTTCCTTACACAAAGTTAAGGGAGTGTTAG
AGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAAAATGTATCAAA
AATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCAGAAATGGAAAAAACCTGCAGT
AAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGTGGTTCTTCAGAAAATAATCACTCTATTAAAG
TTTCTCCATATCTCTCTCAATTTCAACAAGACAAACAACAGTTGGTATTAGGAACCAAAGTGTCACTTGT
TGAGAACATTCATGTTTTGGGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACT
GAAACTTTTTCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAAA
ACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTGACAGATTCTAA
ACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAGGAAATGGTTTTGTCAAATTCA
AGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTGGGAGAACCCTCAATCAAAAGAAACTTATTAA
ATGAATTTGACAGGATAATAGAAAATCAAGAAAAATCCTTAAAGGCTTCAAAAAGCACTCCAGATGGCAC
AATAAAAGATCGAAGATTGTTTATGCATCATGTTTCTTTAGAGCCGATTACCTGTGTACCCTTTCGCACA
ACTAAGGAACGTCAAGAGATACAGAATCCAAATTTTACCGCACCTGGTCAAGAATTTCTGTCTAAATCTC
ATTTGTATGAACATCTGACTTTGGAAAAATCTTCAAGCAATTTAGCAGTTTCAGGACATCCATTTTATCA
AGTTTCTGCTACAAGAAATGAAAAAATGAGACACTTGATTACTACAGGCAGACCAACCAAAGTCTTTGTT
CCACCTTTTAAAACTAAATCACATTTTCACAGAGTTGAACAGTGTGTTAGGAATATTAACTTGGAGGAAA
ACAGACAAAAGCAAAACATTGATGGACATGGCTCTGATGATAGTAAAAATAAGATTAATGACAATGAGAT
TCATCAGTTTAACAAAAACAACTCCAATCAAGCAGTAGCTGTAACTTTCACAAAGTGTGAAGAAGAACCT
TTAGATTTAATTACAAGTCTTCAGAATGCCAGAGATATACAGGATATGCGAATTAAGAAGAAACAAAGGC
AACGCGTCTTTCCACAGCCAGGCAGTCTGTATCTTGCAAAAACATCCACTCTGCCTCGAATCTCTCTGAA
AGCAGCAGTAGGAGGCCAAGTTCCCTCTGCGTGTTCTCATAAACAGCTGTATACGTATGGCGTTTCTAAA
CATTGCATAAAAATTAACAGCAAAAATGCAGAGTCTTTTCAGTTTCACACTGAAGATTATTTTGGTAAGG
AAAGTTTATGGACTGGAAAAGGAATACAGTTGGCTGATGGTGGATGGCTCATACCCTCCAATGATGGAAA
GGCTGGAAAAGAAGAATTTTATAGGGCTCTGTGTGACACTCCAGGTGTGGATCCAAAGCTTATTTCTAGA
ATTTGGGTTTATAATCACTATAGATGGATCATATGGAAACTGGCAGCTATGGAATGTGCCTTTCCTAAGG
AATTTGCTAATAGATGCCTAAGCCCAGAAAGGGTGCTTCTTCAACTAAAATACAGATATGATACGGAAAT
TGATAGAAGCAGAAGATCGGCTATAAAAAAGATAATGGAAAGGGATGACACAGCTGCAAAAACACTTGTT
CTCTGTGTTTCTGACATAATTTCATTGAGCGCAAATATATCTGAAACTTCTAGCAATAAAACTAGTAGTG
CAGATACCCAAAAAGTGGCCATTATTGAACTTACAGATGGGTGGTATGCTGTTAAGGCCCAGTTAGATCC
TCCCCTCTTAGCTGTCTTAAAGAATGGCAGACTGACAGTTGGTCAGAAGATTATTCTTCATGGAGCAGAA
CTGGTGGGCTCTCCTGATGCCTGTACACCTCTTGAAGCCCCAGAATCTCTTATGTTAAAGATTTCTGCTA
ACAGTACTCGGCCTGCTCGCTGGTATACCAAACTTGGATTCTTTCCTGACCCTAGACCTTTTCCTCTGCC
CTTATCATCGCTTTTCAGTGATGGAGGAAATGTTGGTTGTGTTGATGTAATTATTCAAAGAGCATACCCT
ATACAGTGGATGGAGAAGACATCATCTGGATTATACATATTTCGCAATGAAAGAGAGGAAGAAAAGGAAG
CAGCAAAATATGTGGAGGCCCAACAAAAGAGACTAGAAGCCTTATTCACTAAAATTCAGGAGGAATTTGA
AGAACATGAAGAAAACACAACAAAACCATATTTACCATCACGTGCACTAACAAGACAGCAAGTTCGTGCT
TTGCAAGATGGTGCAGAGCTTTATGAAGCAGTGAAGAATGCAGCAGACCCAGCTTACCTTGAGGGTTATT
TCAGTGAAGAGCAGTTAAGAGCCTTGAATAATCACAGGCAAATGTTGAATGATAAGAAACAAGCTCAGAT
CCAGTTGGAAATTAGGAAGGCCATGGAATCTGCTGAACAAAAGGAACAAGGTTTATCAAGGGATGTCACA
ACCGTGTGGAAGTTGCGTATTGTAAGCTATTCAAAAAAAGAAAAAGATTCAGTTATACTGAGTATTTGGC
GTCCATCATCAGATTTATATTCTCTGTTAACAGAAGGAAAGAGATACAGAATTTATCATCTTGCAACTTC
AAAATCTAAAAGTAAATCTGAAAGAGCTAACATACAGTTAGCAGCGACAAAAAAAACTCAGTATCAACAA
CTACCGGTTTCAGATGAAATTTTATTTCAGATTTACCAGCCACGGGAGCCCCTTCACTTCAGCAAATTTT
TAGATCCAGACTTTCAGCCATCTTGTTCTGAGGTGGACCTAATAGGATTTGTCGTTTCTGTTGTGAAAAA
AACAGGACTTGCCCCTTTCGTCTATTTGTCAGACGAATGTTACAATTTACTGGCAATAAAGTTTTGGATA
GACCTTAATGAGGACATTATTAAGCCTCATATGTTAATTGCTGCAAGCAACCTCCAGTGGCGACCAGAAT
CCAAATCAGGCCTTCTTACTTTATTTGCTGGAGATTTTTCTGTGTTTTCTGCTAGTCCAAAAGAGGGCCA
CTTTCAAGAGACATTCAACAAAATGAAAAATACTGTTGAGAATATTGACATACTTTGCAATGAAGCAGAA
AACAAGCTTATGCATATACTGCATGCAAATGATCCCAAGTGGTCCACCCCAACTAAAGACTGTACTTCAG
GGCCGTACACTGCTCAAATCATTCCTGGTACAGGAAACAAGCTTCTGATGTCTTCTCCTAATTGTGAGAT
ATATTATCAAAGTCCTTTATCACTTTGTATGGCCAAAAGGAAGTCTGTTTCCACACCTGTCTCAGCCCAG
ATGACTTCAAAGTCTTGTAAAGGGGAGAAAGAGATTGATGACCAAAAGAACTGCAAAAAGAGAAGAGCCT
TGGATTTCTTGAGTAGACTGCCTTTACCTCCACCTGTTAGTCCCATTTGTACATTTGTTTCTCCGGCTGC
ACAGAAGGCATTTCAGCCACCAAGGAGTTGTGGCACCAAATACGAAACACCCATAAAGAAAAAAGAACTG
AATTCTCCTCAGATGACTCCATTTAAAAAATTCAATGAAATTTCTCTTTTGGAAAGTAATTCAATAGCTG
ACGAAGAACTTGCATTGATAAATACCCAAGCTCTTTTGTCTGGTTCAACAGGAGAAAAACAATTTATATC
TGTCAGTGAATCCACTAGGACTGCTCCCACCAGTTCAGAAGATTATCTCAGACTGAAACGACGTTGTACT
ACATCTCTGATCAAAGAACAGGAGAGTTCCCAGGCCAGTACGGAAGAATGTGAGAAAAATAAGCAGGACA
CAATTACAACTAAAAAATATATCTAAGCATTTGCAAAGGCGACAATAAATTATTGACGCTTAACCTTTCC
AGTTTATAAGACTGGAATATAATTTCAAACCACACATTAGTACTTATGTTGCACAATGAGAAAAGAAATT
AGTTTCAAATTTACCTCAGCGTTTGTGTATCGGGCAAAAATCGTTTTGCCCGATTCCGTATTGGTATACT
TTTGCTTCAGTTGCATATCTTAAAACTAAATGTAATTTATTAACTAATCAAGAAAAACATCTTTGGCTGA
GCTCGGTGGCTCATGCCTGTAATCCCAACACTTTGAGAAGCTGAGGTGGGAGGAGTGCTTGAGGCCAGGA
GTTCAAGACCAGCCTGGGCAACATAGGGAGACCCCCATCTTTACAAAGAAAAAAAAAAGGGGAAAAGAAA
ATCTTTTAAATCTTTGGATTTGATCACTACAAGTATTATTTTACAAGTGAAATAAACATACCATTTTCTT
TTAGATTGTGTCATTAAATGGAATGAGGTCTCTTAGTACAGTTATTTTGATGCAGATAATTCCTTTTAGT
TTAGCTACTATTTTAGGGGATTTTTTTTAGAGGTAACTCACTATGAAATAGTTCTCCTTAATGCAAATAT
GTTGGTTCTGCTATAGTTCCATCCTGTTCAAAAGTCAGGATGAATATGAAGAGTGGTGTTTCCTTTTGAG
CAATTCTTCATCCTTAAGTCAGCATGATTATAAGAAAAATAGAACCCTCAGTGTAACTCTAATTCCTTTT
TACTATTCCAGTGTGATCTCTGAAATTAAATTACTTCAACTAAAAATTCAAATACTTTAAATCAGAAGAT
TTCATAGTTAATTTATTTTTTTTTTCAACAAAATGGTCATCCAAACTCAAACTTGAGAAAATATCTTGCT
TTCAAATTGGCACTGATTCTGCCTGCTTTATTTTTAGCGCTATCACAGGACCCAGAGCCTATGCCCTTTT
AAACTTACCACAAAAGCAGAAGATTAATTCAATTTAAGATGATACTCTCATTTGTTACGTCCTTTTTTTT
TTTTTTTGGAGATGGAGTCTTGCTTTGTCGCCCATGCTGGAGTGCAGTGGCATGATCCTGGCTCACTGCA
GCCTCCACTTCCCGGGTTCACGTAATTCTCCCACCTCAAGCCTCCCTAGTAGCTGGGATTACAGGGACGC
ACCACCATGCCCAGCTAATTTTTGCATTTTTAGTAGAGACTGGGTTTTACCATGTTGGCCAAGCTGGTCT
CAAACTCCTGATGTCAGGTGATCCATCTGCCTCAGCCTCCCAAAGTGCTGGGATTATAGGCGTGAGCCAC
TGTGCCCGGCCAATATTTGTTACTTTCTTAGGTTTAATAGAGAAAAGGGATAAAACATTTCTAACTGGGA
GTTAATTGCATGGAGAAGGTCTTAAATCAGATGTTTTAATGCCTTAAATGTCTGTATAATATCATGTTTT
CAAATCTAATTATAAATACGTTTAAAGCCAAGAATAAATCTTTTAAAAAATTGA

[download]

Replies are listed 'Best First'.
Re: How can I retrieve a DNA sequence from online database using perl code?
by hippo (Archbishop) on Jul 25, 2025 at 12:25 UTC
    in my perl 5.10 version
    ...
    500 SSL negotiation failed:

    5.10 is 15 years old. If your version of openssl (not the perl module, the application library and binaries) is similarly out of date you will have almost no chance of connecting to a modern website using TLS (ie. https).

    Run the code on an up-to-date system as bliako has done and you'll have much better results.

    🦛

[reply]
[d/l]
Re: How can I retrieve a DNA sequence from online database using perl code?
by bliako (Abbot) on Jul 25, 2025 at 09:55 UTC

    FWIW, it works flawlessly on my Linux box with Perl v5.38.2.

[reply]

      Bliako

      Thank you for the information.

      With regards.

[reply]
Re: How can I retrieve a DNA sequence from online database using perl code?
by marto (Cardinal) on Jul 25, 2025 at 09:22 UTC

    "I updated LWP::Protocol::https, IO::Socket::SSL, Net::SSLeay, OpenSSL and Bio modules from cpan (https://www.cpan.org/) inside the lib folder of Perl."

    To be specific, are you doing this manually, as in manually downloading modules from cpan and copying the files? If so this can be a bit of a footgun, consider using cpanm/cpan. Perl 5.10 is from 2007, see Strawberry Perl for a sane distribution for windows.

    Update: from the website NCBI Website Maintenance — Beginning July 25th: "We anticipate this planned outage will last 24 hours or more. During this time, users may experience interrupted access or degraded performance across a range of NLM resources, including databases, search tools, submission systems, and programmatic services."

[reply]

      Marto

      Thank you for your reply. Yes, I have manually downloaded the modules from cpan and copied the files in the lib folder of perl (v5.10) in my laptop. For some specific reasons, I do not want to change the perl version. Please let me know if there is any way to run the program in perl v5.10.

[reply]

        As mentioned, use cpanm (ideally, or cpan) to install the modules properly. Copying files around isn't going to work for modules which aren't pure perl. If your perl stack is that old your local openssl is likely old enough to cause connectivity problems. Running a modern perl on Windows is trivial with the portable releases Strawberry perl provides, see what the release notes list as coming as standard with the distribution.

[reply]

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