Register for upcoming WormBase webinars

The next two webinars “Data mining strategies and workflows” and “Author First Pass and Textpresso” will be held on Feb 22nd and Feb 26th, 2021. Registration is required if you want to attend. Please go to our form to see the complete list of past and upcoming webinars.

WormMart is under redevelopment

We know that several of our users have had problems using WormMart.  We would like to alert users to the fact that WormMart is under redevelopment, some data-sets are  unavailable and there are bugs in the tool that we know of and are actively working on.  Developers aim to build a new release before the end of the year.  We are sorry for this inconvenience.

Did you know that WormBase provides useful data files for download?

WormBase maintains a public FTP site where you can find many commonly requested files and datasets, the WormBase software and prepackaged databases. DNA sequence data for the genomes of C. elegans, C. briggsae, C. remanei, etc., are available in FASTA format, as is protein data.  Microarray data like the up-to-date mapping of microarray probes to WormBase genes for Affymetrix, Agilent, Washington University Genome Sequencing Center and Stanford Microarray Database (SMD) chips, is also made available.  For C. elegans, the following files are down-loadable from the FTP site: confirmed_genes — which lists curated C. elegans genes that have been confirmed by transcriptional data; wormpep — FASTA-format files containing predicted and confirmed protein translations, and many other files.

Take a look at our FTP site at  Be sure to look at the README file in each directory for a listing of the contents of that directory.

Remote access to relational sequence feature databases

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

Host :
Port : 3306
User: remote-user
Pass: none
[tharris@unkar: ~]> mysql -h -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.


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

my $db = Bio::DB::GFF->new(-dsn  => '',
                           -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 And remember, please play nice: this is a shared resource. Egregious use that significantly disrupts other users may be curtailed without warning.