dictyBase News Archive
2003 | 2004 | 2005 | 2006
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, 2006
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!
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