WormBase maintains a public FTP site where you can find many commonly requested files and datasets, the WormBase software and prepackaged databases:
Please see the individual READMEs in each directory describing the contents of the directory. For convenience, select files are directly linked below.
Published datasets hosted at WormBase
For easier distribution of data, WormBase offers to host published datasets. These can be found in the datasets directory on our FTP site. If you would like to host your data at WormBase, please contact [Todd Harris (email@example.com)].
Genomic annotations in GFF format
WormBase provides raw annotations for integration into your own local database. These genomic annotations are distributed in the GFF file format (both versions 1 and 2). Such files can be loaded into a relational schema using the Perl module Mining_WormBase_with_Bio::DB::GFF Bio::DB::GFF. Following the release of a new database from our team at the Wellcome Trust Sanger Institute, some additional post-processing of the GFF files occurs in order to create the variant that we use at WormBase. We use this final file to power the genome browser, dump sequences, generate images on the Gene Summary pages, etc.
You may wish to check the Release_notes for any last minute bugs or issues with the database.
C. briggsae current release post-processed.gff2.gz (waba lines may need to be changed to target Sequence:XYZ instead of CDS:XYZ)
C. remanei current release preliminary_analysis/
C. elegans current release current.gff3.gz
Sequence Data in FASTA Format
C. elegans current release 
C. briggsae current release 
For details of the C.elegans protein set see these WORMPEP pages. This gives a description of the various files included in the WORMPEP release as well as links to download current or previous versions.
All microarray data available in WormBase: ftp://caltech.wormbase.org/pub/annots/microarray/.
Microarray data from specific publications or for a set of probes: http://elbrus.caltech.edu/cgi-bin/igor/microarraytools/dump_microarray_data_mysql.cgi.
Databases and software
The official WormBase software
AceDB, the database that drives WormBase
For your convenience, WormBase offers prepackaged databases that make running your own copy of WorrmBase much simpler. These can be found in the database_tarballs directory on the FTP site.
These prepacked databases include AceDB, C. elegans and C. briggsae GFF databases for MySQL and Blast/BLAT databases. You will probably want to use the current production version of the databases. We also provide access to the development version of the database.
Literature citations, pre-formatted for import into the Endnote citation manager.
All C. elegans citations
WormBook citations ONLY