Power users: you can now remotely access our sequence feature databases.

Host : mining.wormbase.org
Port : 3306
User: remote-user
Pass: none

[tharris@unkar: ~]> mysql -h mining.wormbase.org -u remote-user
Welcome to the MySQL monitor.  Commands end with ; or g.
Your MySQL connection id is 14
Server version: 5.1.45-1-log (Debian)

Type 'help;' or 'h' for help. Type 'c' to clear the current input statement.

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| b_malayi           |
| c_brenneri         |
| c_briggsae         |
| c_elegans          |
| c_elegans_gmap     |
| c_elegans_pmap     |
| c_japonica         |
| c_remanei          |
| clustal            |
| h_bacteriophora    |
| m_hapla            |
| m_incognita        |
| p_pacificus        |
| test               |
+--------------------+
15 rows in set (0.00 sec)

Here’s an example script written in Perl using Bio::DB::GFF.

#!/usr/bin/perl

use Bio::DB::GFF;
use strict;

my $db = Bio::DB::GFF->new(-dsn  => 'dbi:mysql:c_elegans:mining.wormbase.org',
                           -user => 'remote-user',
                           -pass => '',)
  || die "Couldn't establish a connection to remote data mining server: $!";

my $iterator = $db->get_seq_stream(-type => ['coding:exon'] );

# Iterate over all of the requested features
while (my $feature = $iterator->next_seq) {

    # Create a more informative header
    my $name   = $feature->name;
    my $type   = $feature->type;
    my $start  = $feature->start;
    my $stop   = $feature->stop;
    my $strand = $feature->strand;
    my $refseq = $feature->sourceseq; # This is the name of the chromosome
    my $header = ">$name ($type; strand: $strand; $refseq: $start..$stop)";

    # If requested, fetch the sequence of the feature and convert it to fasta
      my $seq  = to_fasta($feature->dna);
      print ">$headern",$seq,"n";
}

# This subroutine converts a dna string into fasta format
sub to_fasta {
  my $sequence = shift;

  # Return if we are already in fasta format.
  return if ($sequence=~/^>(.+)$/m);

  # This is the business part of the subroutine.
  # Place a carriage return after every 80 characters
  $sequence =~ s/(.{80})/$1n/g;
  return $sequence;
}

Questions? Hit me up at [email protected]. And remember, please play nice: this is a shared resource. Egregious use that significantly disrupts other users may be curtailed without warning.