Gene Transfer Format (GTF) files now available

WormBase now provides the canonical gene set for each species in Gene Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html). These files can be used directly by a number of popular sequence analyses tools (e.g. Cufflinks).

The GTF files are available from the WormBase FTP site, for example, the GTF file for C. elegans, c_elegans.PRJNA13758.WS253.canonical_geneset.gtf.gz, is available here.

 

You can find data files on our FTP site

We would like to remind users that our FTP site provides access to various data files.  WormBase has recently improved the organization of it’s FTP site so that users can easily browse and find different data files. We have made nearly every file directly accessible without needing to know what the current version of WormBase is. For example, the following link will always point to the most current release of WormBase:
ftp://ftp.wormbase.org/pub/wormbase/releases/current-www.wormbase.org-release.

You can also access files related to different genomes for a given release, for example you can go to the C. elegans or C. briggsae specific directories.

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 ftp://ftp.wormbase.org/pub/wormbase/.  Be sure to look at the README file in each directory for a listing of the contents of that directory.