Downloads
Warning: The WormBase ftp site is currently undergoing reorganisation so some file/links may be absent/not working.
This page is going to be replace in the near future with an auto generated page that reflects the real data storage.
Please visit Directly for consistent file browsing
Please email help@wormbase.org if you have any trouble finding what you want.
Contents
WormBase maintains a public FTP site where you can find many commonly requested files and datasets, the WormBase software and prepackaged databases:
ftp://ftp.wormbase.org/pub/wormbase/
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 (harris@cshl.edu)].
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 schedule for any last minute bugs or issues with the database.
GFF2
C. elegans current release post-processed.gff2.gz
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 post-processed.gff2.gz
C. brenneri current release post-processed.gff2.gz
C. japonica current release post-processed.gff2.gz
P. pacificus current release post-processed.gff2.gz
GFF3
C. angaria current release current.gff3.gz
B. malayi current release current.gff3.gz
H. contortus current release current.gff3.gz
M. hapla current release current.gff3.gz
M. incognita current release current.gff3.gz
t_spiralis current release current.gff3.gz
The GFF3 format is part of the Sequence Ontology. You can read about it in the GFF3 specification. There is also an online GFF3 validator for checking the validity of GFF3-format files.
Sequence Data in FASTA Format
DNA
Current C. elegans
Current C. briggsae
Current C. remanei
Current C. brenneri
Current C. japonica
Current P. pacificus
Current H. bacteriophora
Current B. malayi
Protein
Current C. elegans protein data
Current C. briggsae protein data
Current C. remanei protein data
Current C. brenneri protein data
Current C. japonica protein data
Current P. pacificus protein data
Current H. bacteriophora protein data
Current B. malayi protein data
Microarray data
Up-to-date mapping of microarray probes to WormBase genes for Affymetrix Agilent WashU GSC SMD chips.
RNAi clone mapping
Up-to-date mapping of Julie Ahringer RNAi library clones to current WormBase gene models: ftp://caltech.wormbase.org/pub/annots/rnai/
Database dumps
Databases and software
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The official WormBase software |
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AceDB, the database that drives WormBase |
Literature citations
Literature citations, pre-formatted for import into the Endnote citation manager.
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All C. elegans citations |
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WormBook citations ONLY |
