[Bioperl-l] GFF MySQL sever failure

Yunlong Liu yunliu at iupui.edu
Sat Sep 25 03:30:13 EDT 2004


Dear all:


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

  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 this.





Yunlong Liu

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