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Welcome to dictyBase, your central resource for the biology and genomics of the social amoeba Dictyostelium discoideum.

News

Temporary closure of the Dicty Stock Center

November 14, 2008 was the last day to place orders or make deposits to The Dicty Stock Center at Columbia University. The week of December 1st, all materials will be transferred to Northwestern University in Chicago. The Stock Center will re-open in early 2009 when funds become available.

November 4, 2008
The January 2009 Database Issue of Nucleic Acids Research will feature an article describing new developments in dictyBase. The open-access paper, dictyBase - a Dictyostelium bioinformatics resource update, is already available.

October 31, 2008
Pictures of the Dicty08 meeting in Tsukuba are now available at dictyBase. Thanks to everyone who contributed. If you have any pictures of this event you'd like to share, send them to us.

October 20, 2008
A Dicty image by Matthew Springer, Stanford University, came in 4th place in the National Geographic Best Microscopic Images Competition 2008. Thanks for bringing this to our attention goes to Paul Fisher, and the picture can also be found on the dictyArt page.

September 11, 2008
We are pleased to announce several new features and data additions to dictyBase.

Graphical visualization of Interpro protein domains has been added to gene pages. Each track in the display is hyperlinked to its source database and upon mouse-over, a tooltip pops up showing the descriptive name of the domain.

We have added a new Gene Identifier for every gene. This Gene ID has the format <<<<<<< index.html DDB_G1234567 and is stable regardless of the curation status of the gene. dictyBase IDs ======= DDB_G1234567 and is stable regardless of the curation status of the gene. dictyBase IDs >>>>>>> 1.157 (DDB1234567) will continue to correspond to sequences associated with genes. The Gene ID is searchable (with usual wildcards) and can be used for linkouts. All automatically created gene names (JCV2_0_XXXXX, BEC6V_2_XXXXX, etc.) and geneDDBXXXXXX names have been replaced with the new Gene ID. From now on, We highly recommend to use the Gene ID for searching, linking and publication purposes.

In collaboration with WormBase, we have implemented Textpresso for Dicty, an information extraction tool for Dictyostelium literature. This enables users to search full text Dicty papers and allows the download of references in multiple formats including EndNote. It can be accessed under the 'Research Tools' dropdown menu.

We have added a new set of EST data kindly provided by Hideko Urushihara and the Dictyostelium cDNA Project in Japan. New ESTs include longer sequence variants (e.g. SSF348) and provide better sequence coverage (e.g. psiB).

Our bulk Downloads section has been updated to include monthly updates of Uniprot2dicty mappings and Interpro protein domains (both text and Excel format). The GFF3 file has now greater coverage of features, which include all ESTs and exon information.

Dictyostelium genes are now searchable by UniProt ID (P07830, Q557E4).

August 5, 2008
We have established a collaboration with UniProt/Swiss-Prot. This effort aims to increase annotations of Dictyostelium proteins in this important protein database. There are reciprocal links between dictyBase and UniProt records, so users have an easy access to complementary information in both databases. We would like to thank Amos Bairoch, Lydie Lane, and all the UniProtKB/Swiss-Prot curators who participate in the Dicty proteome annotation.


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