dictyBase News Archive

2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009

April 16, 2010

In collaboration with Thomas Winckler we now have 471 transposable elements annotated with gene products and descriptions. We also added _RTE and _TE extensions to the gene IDs of retrotransposons and putative DNA transposons, respectively, for easy identification and querying. Have a look at the following examples: DDB_G0277713, DDB_G0291964, DDB_G0267366, DDB_G0294384, DDB_G0270456.

March 31, 2010

We have updated our Mutant Phenotype Download tables to separate terms with pipes instead of the more ubiquitous commas, and we replaced the first column to represent the Strain Systematic Name instead of the Strain ID (these are identical if no Systematic Name is available)

March 29, 2010

We are pleased to announce several new features and data additions to dictyBase

• Interface updates:
  • dictyBase now has a consistent interface throughout the website
  • Updated top menu: links to main resources are grouped into categories. Use the Site Map as a quick reference
  • New pictures and videos are available in the Explore > Pictures/Videos section
• Gene Page updates
  • The Strains and Phenotypes section now contains a list of associated plasmids, e.g. abpC
  • Updated automated gene products based on orthology with human, yeast, and E. coli, e.g. DDB_G0293718
  • Updated Inparanoid links to match Inparanoid Version 7.0 from June 2009
• Plasmids display updates
  • The plasmid details page now contains a link to related gene(s), e.g. pDV-NTAP-CYFP

February 5, 2010

We are pleased to announce that the D. purpureum web portal is now available!

• Access the D. purpureum unassembled contigs via a main page that contains links to the Genome Browser.
• The D. purpureum Genome Browser contains tracks of D. discoideum blast hits that link directly to the dictyBase gene page.
• The BLAST server is now universal, meaning databases from all available genomes are accessible from one and the same page.
• Download D. purpureum sequences and data.
• Search the D. purpureum database for gene IDs (DPU_G0051556), sequence IDs (DPU0052289), or JGI protein IDs (146844).
• Direct access to the D. purpureum database is provided by a link on the dictyBase front page or or from the blue menu top bar under 'Links'.
• For D. discoideum, we added dictyExpress RNAseq links under the Expression section, see an example on the mdhA gene page.

January 22, 2010 There is a nice article about John Bonner, the 'sultan of slime', including a beautiful video. January 20, 2010 We are now adding all deleted, added, or changed gene models to twitter, as soon as they are curated. November 6, 2009 The Franke Dictyostelium Literature database has been updated. Release 18 contains 9455 references. We are very grateful to Jakob Franke for providing this update.

October 21, 2009

Applications for the US to Australia Fellowship Program close on October 31st. The program offers fellowships of up to AU$25,000 to American researchers or students wishing to undertake advanced research or study in Australia.

October 20, 2009

Our paper on the collaboration between dictyBase and Swiss-Prot just came out in the journal Database: Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase (Gaudet et al. 2009).

October 8, 2009

We now have an image of all three D. discoideum life cycles in our Pictures/Video section, kindly provided by David Brown & Joan E. Strassmann.

September 29, 2009

September 22, 2009

It is our pleasure to introduce Bob Dodson who recently started working with us. Bob came from a position as a Bioinformatics Analyst at the J. Craig Venter Institute and has now joined our curator team.

September 9, 2009

At the recent 7thWorld Congress on Alternatives & Animal Use in the Life Sciences in Rome, Robin Williams and Pierre Cosson have been interviewed by the Deutschlandfunk. The resulting radio broadcast from August 31, 2009 can be accessed here (in German).

August 31, 2009

dictyBase is now on Twitter, or get the RSS feed to learn what's new at dictyBase.

August 29, 2009

Download the new dictyBase Quick Resource Guide (PDF)

August 19, 2009

• Thanks to Gadi Shaulsky and Blaz Zupan, we are pleased to announce the availability of dictyExpress, an interactive, web-based exploratory data analytics application providing access to over 1,000 D. discoideum gene expression experiments from the Dictyostelium Functional Genomics Project at Baylor College of Medicine. A direct link to dictyExpress is also provided on many gene pages in under Links, see for example roco4. dictyExpress runs in any Flash 10-enabled web browser and requires no additional installation. We hope you enjoy this tool and please feel free to contact Gadi Shaulsky or Blaz Zupan with suggestions and comments.
• In response to the ever increasing amount of data we represent, and to keep it up in the future, we have done a major update on our Gene Pages. Changes include:
  
  • Grouping all gene related information, such as protein annotations, gene ontology, references and phenotypes into tabs on top of the gene page.
  • Individual sections on the page can be collapsed. Section settings are 'sticky', meaning the browser 'remembers' which sections were open on the last visit.
  • Sections are loaded independently, making the overall page loading faster.
  • Each tab and section contains a question mark icon that displays help hints upon click.
  • A new FASTA button allows fast access to sequences.
  • Different splice variants are accessible via sub-tabs.
  • On the new phenotype tab, strains can be ordered directly by availability by clicking on the shopping cart icon.
  • The BLAST interface has been updated; now sequences are being prefilled when accessing from the gene page or by searching for DDB or DDB_G IDs.
  • Graphics have been added to the BLAST results.
  • We incorporated protein annotations from UniProt on the new protein tab.

Go to your favorite gene or have a look at these examples, piaA, numA.

July 24, 2009

Dicty in the news:An upcoming paper from Paul Fisher's lab to be published in 'Disease Models and Mechanisms' in September is featured in their press release. The paper reports that mitochondrially diseased cells are more supportive of intracellular Legionella replication than wild type cells because of chronic AMPK signalling.

May 13, 2009

We are pleased to announce a new tool and data additions to dictyBase:

• ID converter tool: Given a list of dictyBase IDs (DDB), Gene IDs (DDB_G) or UniProt IDs, this tool converts from one to another. The output comes in two flavours, text and excel formats. To kickstart, try out the example ID's from the hints section.
• E.C. numbers: Our links to the Enzyme Commission now also include the actual EC numbers; see for example the purD gene page.
• We have updated the genome sequence to add a contig that was previously unlocalized, DDB0215037, on the very 5' end of Chromosome 2. As a consequence, DDB0215037 has been replaced by DDB0302697. This was done last December. Note that we have now added 100 N (undefined) residues between this contig and DDB0232463, that used to be the first contig on Chromosome 2 and is now the second one. If you use our GFF3 files and the chromosomal sequence, please note that the coordinates of the genes have been updated accordingly.

May 11, 2009

The 2009 International Dictyostelium Conference will be held from August 23rd to August 28th, 2009, in Estes Park, Colorado, USA, organized by Alan Kimmel and Tian Jin. Visit the website for more information.

April 14, 2009

JBC recently published an article by Raquel Sussman, which describes in passing some of the early days of Dicty. Thanks to Rob Kay for bringing this to our attention.

April 6, 2009

We are pleased to announce the reopening of the Dicty Stock Center at Northwestern University and to introduce Marc Vincelli, who has joined the dictyBase team as the lab technician for the Stock Center. Use the links in the top bar under 'Stock Center' to view, order and submit strains. Thanks to everyone for your continued support - the Stock Center looks forward to serving you.

February 13, 2009

On February 11, 2008, Robin Williams, from the School of Biological Sciences at Royal Holloway, University of London (Ph.D student position available), was one of ten British academic scientists invited to the European Parliament, in Brussels, to present research on reducing the use of animals used in research (Press release). He showed preliminary data identifying Dictyostelium as a potentially suitable model for use in a hierarchy of testing to identify new medicines causing an adverse emetic side effect (vomiting). Using Dictyostelium in this role would potentially reduce the number of animals used in testing new medicinal compounds while also reducing the number of different drugs taken up to final testing, often abandoned due to this common, adverse side effect.

February 12, 2009

Update on the temporary closure of the Dicty Stock Center: We are happy to announce that the NIH has just confirmed that the grant for the Dicty Stock Center has been funded. We cannot provide a firm date as to when we will reopen, but are aiming for mid-March. In the meantime, we'd like to report that the entire strain and plasmid collection has been safely moved from Columbia University to Northwestern University.

December 22, 2008

We are pleased to announce several new features and data additions to dictyBase. Protein domains

• Dictyostelium genes are now searchable by the names of protein domains they contain. Both full or partial matches are possible Results are displayed along with a 'new' icon in the Search summary page and in the Search results page.
• New features and visual enhancements in the graphical display of protein domains. This includes popup balloons with domain names, coordinates, and links to source databases.
• A 'Table view' displays the list of associated domain features, accessible from a link below the protein domain image.

Upgraded Genome Browser

• A new "Gene model" track, showing the best available gene model, replaces the former "Curated Model" and "Gene Predictions" tracks as the default view for gene models.
• Better browsing experience: the genome now can be browsed by dragging the mouse directly over the coordinates shown in the new 'Overview' section (a map of the entire chromosome) and the new 'Region' section (showing the 100kb genomic area containing the sequence centered upon).
• Popup balloons showing gene product information upon mouse-over of the Gene track, and which are clickable linking to the Gene Page and the Gene ontology page.

Gene model curation status:

• On the gene page every Gene Model is tagged with a status note and a graphical icon. Green checkmarks indicate that the gene model has been reviewed by a curator. Gene models not fully supported by either ESTs, mRNA, or sequence similarity have a note followed by a question mark. Genes for which there is conflicting data have a note followed by a red exclamation mark.

Other features

• Updated Pathway tools database along with inclusion of fresh EC links on the Gene Page.
• Downloadable BLAST databases have been simplified and renamed to 'dictyBase Coding Sequences', 'dictyBase Genomic Sequences', and 'dictyBase Protein Sequences'. Those contain the best set of gene models and are updated weekly.
• Searching with the DDB ID now directs to the sequence page, which in turn links to the gene page.
• Downloads site now includes DDB-DDB_G to UniProt mappings, updated monthly.

November 14, 2008

Today 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 DDB_G1234567 and is stable regardless of the curation status of the gene. dictyBase IDs (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.

June 18, 2008

The Dictyostelium Anatomy Ontology. We have been using a new tool in the annotation of phenotypes, the Dictyostelium Anatomy Ontology. The Dictyostelium Anatomy Ontology was developed through a collaboration between dictyBase curators and Jeff Williams from the University of Dundee. For more information, view the summary page we have made, or read the article we have published.

June 16, 2008

Today is the 5th anniversary of dictyBase ! We would like to thank all of you for your support, feedback, and data, which make dictyBase such a great resource even though we are the smallest of model organism databases. We look forward to continue working with all of you for many years.
It is also our pleasure to introduce our new programmer Yulia Bushmanova who is starting today. She is joining Siddhartha Basu to work on our software infrastructure.

April 3, 2008

We now host a new dictyArt page, linked from the side bar of the front page. If you created art inspired by Dictyostelium or you know about an artist who generates dictyArt, please contact dictyBase.

April 1, 2008

Our recent gene predictions, generated using GeneID trained on Dictyostelium curated models, allowed us to identify 71 genes that were not predicted in the current version of the genome and are now curated in dictyBase. Thanks to Rob Kay and Gareth Bloomfield for pointing out several of those genes. You can see the full list on the wiki page.
We also deleted a stretch of DNA located on the floating contig C2F that was redundant with a contig located on C2, removing 24 genes and one tRNA that had been duplicated.

March 21, 2008

dictyBase is featured in the current newsletter of the GSA (Genetics Society of America). See page 16 in this pdf.

February 20, 2008

We are pleased to announce major new data additions to dictyBase.
We have integrated the Dicty_Life analysis of Sawai et al. (2007) that investigates growth, wave formation, and development of REMI mutants by analysing movies taken at different developmental stages. Strains are named in the format V*****. Strains such as V10147 are now searchable in the general search box, and are linked to the affected gene and associated with one or more phenotypes. Clicking on the strain leads to the Strain Details Page, which in turn links to the Dicty_Life mutant movies. These strains can also be found by searching for a phenotype, such as aberrant aggregation. The home page of the Dicty_Life project, which includes links to a search by phenotype and a help page is linked as 'Mutant Movies' in our Research Tool dropdown on every dictyBase page as well as from the Pictures/Video link on the left side bar from our home page.
We have imported a list of predicted regulatory elements kindly provided by Tomaz Curk of the Artificial Intelligence Laboratory, Ljubljana Slovenia. The data is available in the new 'Computationally Inferred Regulatory Elements' section of our gene page, see for example gene ino1. Click on any ID in that section and it takes you to the Regulatory Region Page. The regulatory elements can also be viewed by turning on the 'Putative TF binding site' option in the Genome browser. A smart search for regulatory regions and information about the analysis can be found here.
We added a Curation Status Note to the bottom of all curated Gene Pages. The note informs users about the annotation status and the date when annotations have last been updated.

February 6, 2008

The Stock Center has added a page with 'Additional Materials' to its site. Anybody who has additional reagents that they would like to make available to the Dicty community, please contact us for deposition instructions.

December 17, 2007

dictyBase is now running on brand new servers. Users will notice:

• Improved Performacne
• Improved Stability

Our new servers will also make maintenance easier enabling us to bring you more enhancements in shorter time!
Additionally, we have added a new track to the Genome Browser consisting of Gene Predictions generated with Geneid using a customized training set based on Dictyostelium curated models. To see this track, select 'Geneid Repredictions' in the Tracks section of a Genome Browser page. See here, for example.

November 8, 2007

Paul Fisher has been awarded the Australian Science Prize for his published work on AMPK signaling and its implications in mitochondrial disease. Read the story and the press release! Congratulations Paul!!

September 21, 2007

Pictures of the Dicty07 meeting in Rotenburg are now available at dictyBase. Thanks to everyone who made contributions! If you have any pictures of this event you'd like to share, send them to dictyBase.

September 12, 2007

Thanks to Gerry Weeks, we now have a picture from the 1983 Kyoto Dicty meeting!

July 3, 2007

We have made community annotations more visible and accessible. The links to the community annotation pages have been moved near the top of each Gene Page, in the General Information section. Also, when a community annotation has been added to the gene, a new link in red will appear: "View annotation for..."). For example, see krsA, mcfA. This should make it easier to see when there is a community annotation for a gene of interest. As always we encourage everyone to share their knowledge through the community annotations pages. Learn how to enter your annotations in the Community Annotations Help.

June 18, 2007

April 18, 2007

The web site for Dicty 2007 is now online! The current Featured Community Annotation is the Mitochondrial Carrier Family (MCF) page that describes the 31 members of that gene family. Thanks to Gerard Klein and Michel Satre for providing this information.

March 26, 2007

We are pleased to announce that the Stock Center has re-opened and is ready to fill your orders. Buttons on dictyBase to order strains are functional again. Thank you for your patience! Also thanks to those whose hard work brought the Stock Center back online, and welcome to Zhao Li who will assist with running the Stock Center. In addition, dictyBase has implemented the following improvements:

• Improved searching of ESTs. You can now search based on an EST project clone name. For example: FC-BH04, SSE518, VSF870.
• New and improved strain searching. Strain searches now search more data fields including strain synonyms, systematic names, and strain IDs. For example: fimA-, HG1629, DBS0236175.
• New phenotype search. Simply type a phenotype into the search box to quickly find associated strains, genes and references. For example: abolished aggregation, increased growth rate, aberrant cell morphology.
• Implemented a genetic modification ontology and strain characteristics ontologies for more uniform curation of strains and improved searchability.
• New and improved Genome Browser. You should notice slightly better performance and a nice, new interface for GBrowse.

March 20, 2007

We have an open position for a Biocurator at dictyBase. For more information, please click here.

March 6, 2007

A special symposium on amoebas, for the annual meeting of the British Society for the Study of Protozoology (BSSP), will be held in Warwick on March 29-31. Click here for details.

February 2, 2007

Using Community Annotations, dictyBase users can add their own information about genes in dictyBase. We would like to showcase some of the various ways that the Dicty community is adding to the value of dictyBase by contributing Community Annotations.

• The current Featured Community Annotation is: svkA, contributed by Meino Rohlfs from the Schleicher group.

December 20, 2006

• Phenotypes & Strains Phenotypes are now displayed by strain rather than by gene; each strain is still linked to its modified genes. See, for example, crtA and its associated strains crtA- and crtA-/cnxA-.
• Non-coding RNAs We have added a number of ncRNAs, thanks to Pontus Larsson and the rest of the Soderbom group. New types include snoRNAs, signal recognition particle RNAs, and snRNAs.
• Pseudogenes Pseudogenes now appear as a single track without introns and are no longer translated. This means they will not be found in the "Protein Sequences for dictyBase Primary Features" BLAST database, but they are included in the "Coding" and "Genomic" sequences. The Sequencing Center Gene Predictions are unchanged. See the Pseudogene Page for act30_ps, or click here for a list of pseudogenes in the database.

October 27, 2006

The first molecular phylogeny of all known Dictyostelium species was published in Science today by Pauline Schaap and colleagues (Science, Vol 314, pp. 661-663).

October 16, 2006

Pictures of the Dicty06 meeting in Santa Fe are now available at dictyBase. Thanks to everyone who made contributions! October 4, 2006 The Franke Dictyostelium Literature database has been updated. Release 16 contains 8595 references. Thanks to the efforts of Stephanie Marsh for cross-checking references against Pubmed, and to Miyuki Fukai for translation of Japanese articles.

September 29, 2006

The dictyBase 'Quick Resource Guide' that was distributed at the Dicty 2006 conference is now available for download. If you would like to receive a hard copy of this pamphlet, contact us. The pamphlet can also be downloaded from our Help menu in the blue top bar.

September 19, 2006

In an interview with BBC Radio, Robin Williams discusses the importance of Dictyostelium in biomedical research. Listen here.

September 15, 2006

• Improved Performance We have made changes to our server architecture leading to site-wide performance improvement!
• New and Improved Search In addition to faster searching, the Search Box now searches strains, plasmids, and dictyBase web pages (including the dictyNews) by default. You can also search exclusively for gene names and synonyms to narrow your search.
• tRNAs The tRNAscan program was used to predict tRNA sequences in the Dictyostelium genome. To obtain a list of the 418 tRNAs, search for tRNA*. You can also configure the Genome Browser to view tRNAs.

August 28, 2006

Dicty in the news: Read the Salk Institute press release about Steely2 (stlB), a type III polyketide synthase (PKS) that forges the basic structure of DIF-1.

August 22, 2006

Geneid, a gene prediction program, has recently been trained using dictyBase Curated Models. Run your favorite gene using the web version of geneid available here. Paste a genomic FASTA sequence in the box, select 'Dictyostelium discoideum' as your organism, and click 'Submit.' Several output options are available at the bottom of the page. Many thanks to Francisco Camara for incorporating Dictyostelium into this very useful tool!

July 26, 2006

Protein Domains: Updated analysis We have re-run InterProScan on the Dictyostelium proteome and updated electronic Gene Ontology annotations accordingly. You can download the new version of the InterPro domains of Dictyostelium proteins on the Downloads site.

July 25, 2006

• Biochemical Pathways Users can now visualize known pathways associated with a gene. On the Gene Page of genes that play a role in metabolic pathways, a new section on the Gene Page displays the names of the pathways the gene is involved in (see pgkA). The pathway display is generated by the Pathway Tools software from SRI.
• DictyWiki: A community annotation tool Users can now play an active role in annotation! Each Gene Page has a 'Community Annotations' link. This will open up a new window and present a page that can be edited to contain any information that a researcher sees fit to report. For example please see the wiki page (like Wikipedia) for sibA or rnrB.

July 17, 2006

N-terminal myristoylation analysis: We have a list of 103 proteins predicted to have a N-terminal myristoylation site. You can find this information on the Downloads page or directly here.

June 16, 2006

dictyBase is now three years old and has grown quite a bit over the years. We thank all our users for their contributions and encouragement and the NIH for financial support.

May 8, 2006

We have recently completed our latest whole genome GenBank submission. The project's accession number in GenBank is AAFI00000000. The curated models and annotations in GenBank are now current with dictyBase from March 10, 2006. All genomic DNA in GenBank shares the common coordinate system used by dictyBase from version 2.5 of the Dictyostelium genome.

May 5, 200

6 Warning: Due to a bug in our software, the genomic sequence for a number of genes was mis-reported on the sequence page. All sequences are now represented correctly, please see the details here.

May 3, 2006

We have recently heard from the NIH that the dictyBase grant application will be funded for another four years. Thanks for all of your support! We look forward to continuing to serve you.

April 21, 2006

We are pleased to inform you that the Dictyostelium kinome is now available at kinase.com. The KinBase database at kinase.com allows you to browse Dicty kinases by name or classification, download sequences, and view functional protein domains. Every Gene Report page includes a link to the corresponding dictyBase Gene Page. See, for example, the PKA Gene Report. In addition, KinBase contains all kinases from the human, mouse, fly, worm, and yeast genomes, providing an easy and efficient method for side-by-side comparison. Enjoy!

March 14, 2006

We are pleased to announce the release of dictyMart! dictyMart provides advanced search capabilities that greatly enhance users' ability to easily find information about genes of interest. Currently the tool supports batch downloads of Gene Ontology annotations, exon positions, sequences and much more. To access dictyMart, click on the dictyMart link in the toolbar at the top of every page. To familiarize yourself with the dictyMart interface, we recommend watching our tutorial on the dictyMart help page. dictyMart is created with software from the BioMart project. For more information on BioMart please visit their website: http://www.biomart.org.

March 9, 2006

In an effort to improve the integration of the Dicty Stock Center into dictyBase, we have linked the strains in the Stock Center with their corresponding genes. See, for example, the JS64 strain in the Dicty Stock Center. Likewise, the Gene Pages for tipA and tipB link to the appropriate strains in the Stock Center. We hope that this new feature will be useful in your research and improve your navigation in dictyBase and the Dicty Stock Center.

December 12, 2005

Additions to the Download Site:

• Protein domains predictions from InterProScan for our primary sequence dataset. Note that the protein domain analysis run by GeneDB at Sanger can be viewed by clicking on the "Predicted Protein Domains at GeneDB" in the "Protein Information" section of every Gene Page.
• Genes on the AX3/AX4 Chromosome 2 duplication.
• Genes disrupted by the Baylor College of Medicine Insertional Mutants Project.

December 2, 2005

• Genome update: Version 2.5. The latest update to the genome from the Sequencing Centers has been implemented in dictyBase. There have been numerous gap closures and base call corrections. The vast majority of the gene models (99.8%) remain unchanged, however, some genes have minor changes to the sequence. A list of all the genes that have been affected by the update can be viewed here.
• Alert for genes on the Chromosome 2 duplication. We have added an alert to all Gene Pages of genes that are located on the Chromosome 2 duplication. For example, see the Gene Page for carA and its duplicate DDB0217181. You can view lists of the genes present on the first repeat and on the second repeat.

October 11, 2005

We have made efforts to increase the performance of dictyBase such that most pages should load at least twice as fast. The most significant improvements will be seen when loading the Gene Page. Please visit your favorite database pages and send us feedback, good and bad.  If you encounter problems, please include information about the web page you are viewing and the web browser you are using. Thank you!

September 30, 2005

We are pleased to announce a new page where you can download Tools for dictyBase that have been designed by our users. A link to this page can also be found on our new Downloads page. Colleagues who have written applications they think would be useful for the community are invited to send them to dictyBase.

September 20, 2005

Pictures of the Dicty05 meeting in Autrans are now available at dictyBase http://dictybase.org/DictyAnnualConference/. Thanks to everyone who made contributions!

August 5, 2005

We are pleased to announce the inauguration of the dictyBase Downloads site, which can be accessed from the left-hand side menu of the Home Page. The Downloads site is a repository of files containing:

• Functional annotations of all the Dictyostelium genes (dictyBase ID, gene names, synonyms, and gene products)
• Lists of curated Dictyostelium mutants;
• Gene Ontology association file;
• GFF3 files: GFF3 allows us to not only distribute the sequence, but also the position of our gene predictions and curated models as well as some of the curated annotations. The GFF3 specification can be found at: http://song.sourceforge.net/gff3.shtml

The Downloads page also links to our Download Sequences site and the Franke Dictyostelium Reference Library site.

July 26, 2005

We now have links to the AAAS Signal Transduction Knowledge Environment (STKE). Reciprocal links take dictyBase users to the signal transduction pathways curated at STKE, and bring STKE users to dictyBase Gene Pages. Check out dagA or mlkA and click on STKE in the Links section. To access the STKE pages, you need to register (free).

May 9, 2005

We are pleased to pass along the word that Peter Devreotes has just become a new member of the National Academy of Sciences, one of the highest honors that can be awarded to a U.S. scientist. Congratulations, Peter!

May 6, 2005

On behalf of the International Dictyostelium genome sequencing consortium we are pleased to announce that the Dictyostelium genome paper was published in this week's issue of Nature.

May 2, 2005

dictyBase has undergone a major software upgrade. Although hopefully none of our users will notice, since everything should work as before, we have made major changes to the underlying database that will enable us to capture many more features of the genome, RNAs, repeated elements and 5' and 3' non-coding regions. You should start to see the new types of information begin to appear in dictyBase over the next few months. The database schema being implemented is called 'Chado' and is developed by the Generic Model Organism Database (GMOD) project.

March 15, 2005

The Dictyostelium review articles have been updated in the 'Learn about Dictyostelium' section.

March 9, 2005

We are pleased to announce that the Dicty Stock Center now houses a collection of more than 100 plasmids. The new plasmid catalog currently shows a listing of 51 of the plasmids available at the Dicty Stock Center. We will continue to add plasmids to the catalog. Information about sending plasmids can be found here.

March 2, 2005

• Thanks to Larry Blanton and Mark Grimson, dictyBase now hosts their Dictyostelium pictures for viewing and to download. These pictures, as well as all Dictyostelium videos, can be accessed by clicking on our new Pictures/Videos link in the left side menu.
• We now have all ListServ discussions since 1997 archived, which is available through our new ListServ link in the side menu.
• There is a new Search dictyBase link in the side menu. This page allows you to search the dictyNews and all dictyBase web pages or search the database for genes, gene products, colleagues, authors, etc. all in one place.

February 15, 2005

A shopping cart system is now in place to order strains from the Dicty Stock Center. Click on any strain in the Strain Catalog and on the Strain Details page (e.g. AX3-K). Just add the strain(s) to the shopping cart and proceed to checkout.

January 12, 2005

We have updated our Links to Dicty Labs. Feel free to check it out and let us know if any lab website has been overlooked!

December 16, 2004

Correction to Primary Sequences Sets: For the past two weeks, the "Primary Features" sequence sets have included GenBank records in addition to our real primary features. This means that these sequence sets contained significant redundancy. We have now corrected the problem and recommend that you download the "fixed" version of the "Primary Feature" if you have downloaded it in the past two weeks. Please note that we update these everyday, so it is a good idea to download them on a regular basis. More information on the sequences available at dictyBase can be found in the Help pages.

November 19, 2004

The Franke Dictyostelium Literature database has been updated. Release 15 contains 8132 references. Thanks to the efforts of Stephanie Marsh, the entire database now contains the PubMed ID numbers, when available. We also thank Miyuki Fukai for providing a translation of the biography of several Japanese language articles.

October 22, 2004

We have added links to insertional mutants at Dicty Ensembl. You will find the links in the 'Strains and Mutants' section on the Gene Page. Check out your favorite gene or have a look at the adprt3 gene.

October 18, 2004

As part of the Pioneers series in Trends in Cell Biology, there is an article this month honoring Günther Gerisch's lifelong achievements in Dictyostelium research. The article, written by authors who at some point passed through the Gerisch Cell Biology Department at the Max Planck Institute in Martinsried, Germany, highlights the enormous impact of Gerisch's decision to study the role of the actomyosin cytoskeleton in chemotactic motility.

October 7, 2004

Pictures and abstracts of the Dicty04 meeting are now available in dictyBase http://dictybase.org/dictyconf.html.

September 2, 2004

We have added links to protein domain information at GeneDB. You will find the links in the 'Protein Information' section on the Gene Page. Check out your favorite gene or have a look at these examples: hstA, casK.

August 10, 2004

We have made a major update to dictyBase. We have reorganized the way sequences are linked to genes and displayed. Our new Gene Page lists all the sequences associated to a gene, including ESTs, by category. Each sequence has a separate Sequence Info Page, where additional information, including nucleotide and protein sequence, can be found. The Gene Page now includes a larger map for instant viewing of the alignment of Gene Models, GenBank genes or mRNAs, and ESTs. Clicking anywhere on that map takes you to the Genome Browser, as before. We have also introduced a line of Navigation Links on the top of each page, which makes it easy to navigate from the Sequence Page back to the Gene Page, or from both to the appropriate coordinates on the Genome Browser. Have a look at your favorite gene or at these examples (dagA, cak1). For more information refer to the Gene Page Help and the Sequence Page Help. Please send comments and suggestions here.

July 7, 2004

We are pleased to announce that dictyBase now has direct links to the Japanese Atlas database for in situ expression data on 150 locus pages. The link can be found on the locus page (e.g. cbpA, mlkA, carA) under 'Expression Information'. For a detailed description please see the Project Overview and Maeda et al. (2003).

June 23, 2004

Thanks to the generosity of the Dictyostelium Genome Sequencing Consortium, dictyBase now contains Version 2 of the complete Dictyostelium genome. In this release all gene predictions have been automatically annotated with gene products. We also updated our Genome Browser with several more track options such as GC content and frame usage.

June 16, 2004

dictyBase, the unification of the former Dicty WWW Server and the new database, celebrates its first birthday today!

March 26, 2004

• The nuclear-encoded genes published in GenBank have been mapped to chromosomes, and Curated Models have been added whenever possible. We have now started to curate Gene Predictions where there is supporting data such as ESTs and/or sequence similarity. These loci are being upgraded with a Curated Model, Locus Name, Gene Product, Description, GO annotations. There are currently 857 Curated Gene Models.
• The sequence data in dictyBase can now be downloaded. The download site is http://dictybase.org/db/cgi-bin/dictyBase/download/blast_databases.pl. The sequences of full chromosomes can be downloaded, or genomic, coding sequences or predicted proteins. There is help explaning what sequences each database contains.
• Improved alignments on the EST and GenBank tracks of the Genome browser: Only the longest continuous alignment is now shown, eliminating some misleading smaller hit regions and some misleading breaks in the alignments. The algorithm used is described in: "Alignment of BLAST High-scoring Segment Pairs Based on the Longest Increasing Subsequence Algorithm" Zhang H, Bioinformatics, 19:1391-1396, 2003.

March 3, 2004

• dictyBase is now searchable by dictyBaseIDs. The dictyBaseID is located on the left-hand column, last row of the Locus Page under "Primary dictyBaseID". It always begins with DDB followed by seven numbers. You need to type the entire dictyBaseID, that is, DDB plus the 7 digits in the search box to retrieve a page. There is more information on the Locus Page Help.
• NCBI and SRS (Sequence Retrieval System, hosted at EBI) have added links to dictyBase. Therefore, SwissProt entries should have links to their corresponding dictyBase Locus Page. Also, on GenBank nucleotide records, clicking on the "LinkOut" option displays a link to dictyBase Locus Pages.

February 20, 2004

dictyBase now contains and can display the data from two large scale gene expression experiments. We would like to thank The Baylor Functional Genomics team lead by Gad Shaulsky, John Halter and Adam Kuspa, and Negin Iranfar, Danny Fuller, and William Loomis at UCSD for providing the data. Each dataset has expression profiles for over 3,000 genes. To see the data, go to any locus (accessed by the search box at the upper right corner). If there is expression data for that gene, you will see an item called "Expression Information" on the right side of the page. A pull-down menu allows you to select either the UCSD or the Baylor data (when both available; some loci will only have one of the two). Example of loci you can look at are: rnrB, mlcE, and cotB.

January 30, 2004

Thanks to the generosity of the Dictyostelium Genome Sequencing Consortium, we are pleased to announce that dictyBase now contains the complete Dictyostelium genome sequence, including chromosomes 1, 2, 3, 4, 5, 6, and the mitochondrial genome. The genome is annotated with both HMM gene predictions provided by Negin Iranfar, Rolf Olsen and William Loomis (11,984) and gene predictions from the Sequencing Consortium (13,230).

January 23, 2004

• The Stock Center strains are now part of the dictyBase database. The Strain Catalog has a new look, with links to a Strain Details Page for each strain. The "Order this Strain" button on the Strain Detail Page sends an e-mail to Jakob Franke who will process the order.
• The Stock Center's Search Tool is now available. Strains can be searched by name, strain ID, strain type, genotype, phenotype, species, mutagenesis method, parental strain, plasmid, depositor, or a keyword.
• The Franke Dictyostelium Reference Database has a new update, Update24. Beginning with the records in Update23, PMID numbers have been included whenever available.

January 15, 2004

Thanks to the generosity of the Dictyostelium Genome Sequencing Consortium, we have now added the EUDICT region of Chromosome 6, that is, roughly half of that chromosome. dictyBase now contains the full sequence of Chromosomes 1, 2, 4, 5, 6 and the mitochondrial genome. We expect the complete genome sequence to be available on dictyBase very shortly. Look again soon for updates!

December 9, 2003

The organizing committee for the 2004 International Dictyostelium Conference has launched the Website for Dicty 2004.

November 25, 2003

• Thanks to the generosity of the Dictyostelium Genome Sequencing Consortium, dictyBase now contains genome sequence for Chromosomes 1, 2, 4, 5, the Baylor region of Chromosome 6 (2.1 Mb), and the mitochondrial chromosome. There are more than 9,000 gene models aligned with the corresponding ESTs and HMM Gene Predictions.
• The feature type 'Verified Gene' was replaced with 'Curated Model'. A Curated Model has been manually inspected and updated when additional data such as a GenBank cDNA, genomic DNA, or multiple ESTs provide supporting data. Specific information about the data supporting the Curated Model can be found in the Locus Notes on the Locus Page.
• All sequence data is now graphically displayed in our Genome Browser. Each sequence type is shown as a separate track: Curated Models, Gene Predictions from Sequencing Centers, EST Alignments, and HMM Gene Prediction Alignments. We have now added "GenBank mRNA (cDNA) Alignments" and previously characterized gene sequences called "CDS from GenBank Genomic Fragments Alignments". Note that tracks labeled 'Alignments' are based on BLAST hits. Due to the BLAST parameters used, the display may show breaks where none actually exist. We encourage users to do pairwise alignments if there is interest in a particular gene.
• We have also added direct links to NCBI BLAST. Thanks to a great suggestion by Robert Insall there is now a link 'BLASTP at NCBI' in the BLAST drop-down menu on the Locus Page. This automatically pastes the protein sequence into a NCBI query window allowing users an easy way to identify potential homologs of Dictyostelium genes in other organisms. There is also a link 'BLAST at NCBI' from our BLAST server.

November 10, 2003

• Research Tool added: dictyBase is now curating phenotypes. A list of developmental mutants includes gene names (linked to the locus page), references (linked to the PubMed record) and phenotype information. We are using a restricted vocabulary to describe phenotypes. This allows ready comparison of phenotypes between different mutants. Phenotype information is also shown on the locus page along with details about the type of mutation that produces the phenotype. Clicking on 'Phenotype details and references' leads to a detailed list of phenotypes for the locus queried (example). Clicking on a specific phenotype opens a referenced list of curated loci, whose mutation(s) result in that phenotype (example).

October 2, 2003

• We have added Feature Type information for all the sequences in dictyBase. The sequences are now identified as either: Gene Model from Sequencing Centers, Verified Gene, Genomic Fragment, mRNA, EST, or HMM gene models. Read more about the sequences available in dictyBase here.
• The different Feature Types are displayed on separate tracks on the Genome Browser. This allows the simultaneous visualization of sequences from different sources.
• The Locus Page of ESTs and HMM gene models now have links to additional sequence information.
• Added functionality to the Sequence Analysis Tools on the Locus Page: All the BLAST options are now available directly from the Locus Page. The sequence selected in the "Retrieve Sequence" pull-down menu gets pasted automatically in the dictyBase BLAST server and the appropriate BLAST program is selected.
• We have added a form for submitting abstracts of manuscripts accepted for publication to the dicty newsletter. This form can be accessed from the left-hand side menu.

September 18, 2003

Dietmar Manstein announces a new Special Dictyostelium Issue (including a CD with movies) of the Journal of Muscle Research and Cell Motility. More information and the order form can be downloaded here (pdf).

August 20, 2003

The dictyBase BLAST server is updated and now allows users to compare any query sequence to six different D. discoideum sequence data sets . All BLAST programs (blastn, blastp, blastx, tblastn, and tblastx) are now available. [Go to BLAST]

July 31, 2003

Jakob Franke wrote 'A short history of axenic strains in Dictyostelium discoideum', available under Research Tools -> Dictyostelium Strains. The Dictyostelium review articles have been updated in the 'Learn about Dictyostelium' section.

July 30, 2003

Pictures of the Dicty Down Under meeting are now available in dictyBase. http://dictybase.org/DictyAnnualConference/dicty03/index.html].

July 09, 2003

dictyBase was chosen to be the Science Model Organism Database of the Month! [http://www.sciencemag.org/feature/plus/sfg/resources/res_model.shtml].

June 23, 2003

Thanks to the Baylor Sequencing Team, we now have the 2.1 Mb segment of chromosome 6 available in dictyBase!

June 20, 2003

Science has just published on its STKE web site two Connection Maps describing cAMP signaling pathways in Dictyostelium. Have a look here!