[Bioperl-l] Help needed on GFF

Yunlong Liu yunliu at iupui.edu
Sat Sep 25 17:15:08 EDT 2004

I am new in both bioperl and database.

Can anyone help me to solve this problem?


I was trying to retrieve sequences from a specific region on the human genome, for instance, chr2, 1 - 10000.

I am using Bio::DB::GFF to solve this.  I copied the following script from http://doc.bioperl.org/releases/bioperl-1.4/Bio/DB/GFF.html#SYNOPSIS


use Bio::DB::GFF;

# Open the sequence database
  my $db      = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt',
                                   -dsn     => 'dbi:mysql:elegans',
                                  -fasta   => '/usr/local/fasta_files'
  # fetch a 1 megabase segment of sequence starting at landmark "ZK909"
  my $segment = $db->segment('ZK909', 1 => 1000000);



However, I got the following error message:


DBI connect ('elegans', '',.) failed: Can't connect to MySQL server on 'localhost' <10061> at C:/Perl/site/lib/Bio/DB/GFF/Adaptor/dbi/caching-handle.pm line 139.


Can anyone help me to solve it?




Yunlong Liu

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