The WormBase genome browser now contains over 100 tracks of functional data from the ModENCODE Project. Please visit ModENCODE to search and download the underlying data sets.
Biological Curator position with WormBase at Caltech
Biological Curator position is now available at WormBase-Caltech. Please contact Paul Sternberg (pws@caltech.edu) for more information.
Remote access to relational sequence feature databases
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 todd@wormbase.org. And remember, please play nice: this is a shared resource. Egregious use that significantly disrupts other users may be curtailed without warning.
New release of the database: WS214
WormBase has been updated to the WS214 release of the database. New in this release: data from the modENCODE Project, available as tracks on the C. elegans Genome Browser.