Downloads

From WormBaseWiki
Jump to: navigation, search

Warning.jpg Warning: The WormBase ftp site is currently undergoing reorganisation so some file/links may be absent/not working. Warning.jpg

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.

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

The official WormBase software

ftp://ftp.wormbase.org/pub/wormbase/software

AceDB, the database that drives WormBase

http://www.acedb.org

Literature citations

Literature citations, pre-formatted for import into the Endnote citation manager.

All C. elegans citations

current-wormbase-literature.endnote.gz

WormBook citations ONLY

references.txt