Recent changes and updates to SUPERFAMILY.
| 18th August 2008 |
Added domain assignments for over 50 bacterial genomes from the
NCBI.
Highlights include, the first genome to be sequenced from what may become a new bacterial phylum
Elusimicrobium minutum Pei191, new genomes
from the Verrucomicrobia phyla
Akkermansia muciniphila ATCC BAA-835,
Methylacidiphilum infernorum V4
and the Aquificae phyla
Sulfurihydrogenibium sp. YO3AOP1,
Hydrogenobaculum sp. Y04AAS1.
|
| 8th August 2008 |
Integrated domain assignments for new green algae
Ostreococcus RCC809.
Note: There does not appear to be an associated NCBI taxonomy
identifier for this genome. Using the Ostreococcus genus identifier for now.
Update: NCBI taxonomy identifier now available for this genome and
integrated.
|
| 30th July 2008 |
Integrated Christine Vogel's functional annotation.
Christine annotated domain superfamilies with respect to their usual role in a protein,
in a particular pathway or in the cell/organism. She prepared a scheme of 50 detailed
function categories which map to 7 more general function categories.
For example, C2H2 and C2HC zinc fingers superfamily
and Globin-like superfamily.
|
| 11th July 2008 |
New documentation:
how to download, install and use the SUPERFAMILY database.
A description of how to download the MySQL database dump, install it and query it. Each of the
database tables are described and a diagram showing the relationships between the database tables
is included.
|
| 3rd July 2008 |
Domain assignments for 2 new fungal genomes from the
JGI:
Trichoderma atroviride and
Cochliobolus heterostrophus.
Trichoderma atroviride is best known for its biocontrol capabilities
against a range of phytopathogenic fungi, which are pests of hundreds of plant crops.
Trichoderma atroviride has caused major crop losses in the past.
|
| 23rd June 2008 |
Loaded domain assignments for the
TargetDB sequences.
TargetDB is a structural genomics target registration database, which provides
status and tracking information on the progress of the production and solutions
of 3D protein structures. TargetDB contains over 175,000 sequences from 25
contributing sites.
|
| 20th June 2008 |
Loaded domain assignments for the microalgae
Chlorella sp. NC64A, which is
a model system for studying DNA virus/algal interactions.
|
| 19th June 2008 |
Added a page describing how to download,
install and run the SUPERFAMILY hidden Markov models and associated scripts.
|
| 2nd June 2008 |
Added 10 Eukaryotic genomes, and updated 12 drosophilid genomes.
Including several newly sequenced fungal strains such as the Chytridiomycota
Batrachochytrium dendrobatidis JAM81,
early releases of the disease vector
Ixodes scapularis (tick)
and the livestock pathogen
Trypanosoma congolense.
|
| 12th May 2008 |
Added the transgenic papaya (Carica papaya) genome, and over 50 prokaryote genomes.
Highlights among the prokaryote genomes include the first genome from the Verrucomicrobia order (Opitutus terrae) of bacteria, and
the first genome from the Korarchaeota order (Candidatus Korarchaeum cryptofilum) of archaea.
|
| 30th Apr 2008 |
Added the phytoplankton Emiliania huxleyi, which
is of interest because of it's production of polyketides with antimicrobial, antifungal, antiparasitic, antitumor and
agrochemical properties. Updated the beetle Tribolium castaneum
assignments as analysis of the genome sequence recently became available
[ ].
Updated the Schizosaccharomyces pombe genome for a fungi researcher.
|
| 28th Apr 2008 |
Modified taxonomic position of the Monosiga brevicollis,
Dictyostelium discoideum and
Entamoeba histolytica eukaryotic genomes.
Monosiga brevicollis now occurs between the metazoa and fungi [].
Both Dictyostelium discoideum []
and Entamoeba histolytica []
now occur between the fungi and remaining eukaryotes.
|
| 22nd Apr 2008 |
Loaded domain assignment results for viral sequences from the
NCBI.
|
| 15th Apr 2008 |
Integrated InterPro abstracts and
Gene Ontology (GO) terms.
For example:
Cytochrome c,
Mitochondrial carrier,
Sigma3 and sigma4 domains of RNA polymerase sigma factors.
InterPro have added abstracts for 1,052 superfamilies, and 763 superfamilies have some gene ontology annotation.
|
| 11th Apr 2008 |
Loaded 2 new early release plant genomes:
Glycine max (Soybean) and
Zea mays (Maize).
|
| 8th Apr 2008 |
Major update of all Ensembl genomes, including new genomes:
Horse and
Orangutan.
|
| 31st Mar 2008 |
Added new plant genome from the JGI:
Sorghum bicolor.
|
| 18th Feb 2008 |
Added 2 new algae genomes from the JGI:
Micromonas sp. RCC299,
Micromonas sp. CCMP490.
|
| 23rd Jan 2008 |
Added 3 fungal genomes, 59 bacteria and updated UniProt.
|
| 10th Jan 2008 |
Added 1 plant and 7 fungal genomes:
Selaginella moellendorffii (Spikemoss),
Vanderwaltozyma polyspora,
Podospora anserina,
Trichoderma virens,
Saccharomyces cerevisiae YJM789,
Saccharomyces cerevisiae RM11-1a,
Cryptococcus neoformans var. grubii H99,
Cryptococcus neoformans B-3501A.
|
| 18th Dec 2007 |
Updated the mouse genome and added 2 new animal genomes:
Microcebus murinus (mouse lemur),
Ochotona princeps (American pika).
|
| 13th Dec 2007 |
Web site re-design goes live. Please report any inconsistencies or errors to
superfamily@mrc-lmb.cam.ac.uk.
|
| 6th Dec 2007 |
Post-doc postion to work with
Julian Gough on SUPERFAMILY available.
Enquiries to Julian Gough.
Update: position has been filled.
|
| 12th Oct 2007 |
Added 10 new Eukaryotic genomes:
Aureococcus anophagefferens,
Giardia lamblia,
Helobdella robusta,
Capitella sp. I,
Nasonia vitripennis,
Trichoplax adhaerens,
Vitis vinifera,
Toxoplasma gondii,
Xenopus laevis,
Mycosphaerella fijiensis.
|
| 1st Oct 2007 |
Completed inclusion of 200 new, and 100 updated, prokaryotic genomes.
|
| 7th Sept 2007 |
Exciting new tool for the visualisation of domains across genomes.
On every page that lists the number of domains in each genome for a given superfamily (or family),
there is a new link to a tool called "TaxViz". TaxViz provides a graphic representation of the
occurence of a domain across all the taxonomic kingdoms included in SUPERFAMILY.
|
| 21st Aug 2007 |
Family level data and analysis has been extended to include: pages listing family assignments
for each genome, and unusual (over- and under-represented) families within each genome.
|
| 9th July 2007 |
Added more new low coverage vertebrate genomes from Ensembl,
fungal genomes from FGI and basal metazoa from
JGI. Highlights include the
sea anemone Nematostella vectensis,
crustacean Daphnia pulex ,
moss Physcomitrella patens subsp. patens and
the colony forming algal species Volvox carteri f. nagariensis.
|
| 11th May 2007 |
Added 4 new low coverage vertebrate genomes from Ensembl:
Cavia porcellus,
Myotis lucifugus,
Spermophilus tridecemlineatus,
Otolemur garnettii.
|
| 4th April 2007 |
Added 7 new low coverage vertebrate genomes from Ensembl:
Dasypus novemcinctus,
Echinops telfairi,
Erinaceus europaeus,
Felis catus,
Loxodonta africana,
Oryctolagus cuniculus,
Tupaia belangeri.
|
| 12th Mar 2007 |
Updated to current (43.36e) Ensembl homo sapiens genome.
|
| 19th Feb 2007 |
InterPro update to SUPERFAMILY 1.69.
|
| 4th Jan 2007 |
Added 11 AAA drosophilid genomes to the web site and database:
Drosophila ananassae,
Drosophila persimilis,
Drosophila virilis,
Drosophila simulans,
Drosophila mojavensis,
Drosophila yakuba,
Drosophila sechellia,
Drosophila grimshawi,
Drosophila erecta,
Drosophila pseudoobscura,
Drosophila willistoni.
|
| 11th Dec 2006 |
Moved SUPERFAMILY website and database to new server.
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