SUPERFAMILY news on TWITTER:
From now on please refer to twitter in order to stay up to date with our news. Follow us @SUPERFAMILY.
2nd August 2011
SUPERFAMILY online user survey:
We are always looking for ways to improve the SUPERFAMILY resource and now is your chance to help. We have just launched our first online user survey to get your feedback. It will take just a few minutes to fill out and it will help shape the future of SUPERFAMILY. To take the survey click here.
1st August 2011
SUPERFAMILY is recruiting:
We are looking for a post-doctoral research associate to help develop and improve existing features of SUPERFAMILY. For more details click here.
5th July 2011
SUPERFAMILY newsfeed is back!:
Sorry that the news feed has been so quiet for so long but now we are back! We have been busy
and SUPERFAMILY has many new features which are summarised below:
Ancestral Nodes: For example the ancestral node for all Eukaryota can be seen here.
Updated to SCOP 1.75: Details of this release can be found on the SCOP website.
HMMER 3: We are now using HMMER 3 for model scoring.
MySQL schema restructuring: The details of the new schema can be found here.
Over 1700 Genomes: The genomes can be viewed here.
GO/Phenotype Ontologies: All domains and supra-domains are now annotated with GO and Phenotype information.
20th May 2010
Loaded domain assignments for 120 bacteria and archaea:
Made the genome and superfamily searches live on the compare genomes page http://bit.ly/hoSGU
Hope this improves web site usability
29th June 2009
Added 5 genome and superfamily shortcut searches to comparative genomics page:
There are quite a few specialised comparative genomics functions on the SUPERFAMILY site,
but they are all deeply embedded in the web site hierarchy.
To help rectify this problem we have added 5 genome and superfamily search options.
So, it should no longer be necessary to browse through over 1,000 genomes or 1,800 superfamilies.
We hope these shortcut searches help to make the comparative genomics functionality on the web site more usable.
12th June 2009
Monthly twitter roundup:
Using some of the maatkit tools http://www.maatkit.org/
to find and fix slow SQL on the web site
Loaded annotation for Hydra magnipapillata http://bit.ly/d2JKG
which is a fresh water animal that may age very slowly
New SCOP release http://bit.ly/c2lPy
Roughly 200 new superfamilies Covers PDB up to 23/02/09
Job vacancy: Post-doctoral position (Research Associate) to work on SUPERFAMILY and related research.
Official application procedure.
Please contact Julian Gough (homepageemail) for further information before applying.
30th Apr 2009
Added 1.73 domain assignments for UniProt:
Domain assignments for the major 15.0 release of UniProt
have been loaded into the database and onto the web site.
They will be available for download, from the ftp site, on Monday 4th May.
The percentage of sequences with one, or more, domain assignment is 60 %.
6th Mar 2009
Over 1,000 organisms included in SUPERFAMILY:
The recent addition of several hundred bacterial genomes and 15 fungal
strains, means there are over 1,000 organisms in the SUPERFAMILY
database.
The sequence of the first complete genome sequence of a termite gut symbiont - an uncultured bacterium named Rs-D17 belonging to the candidate phylum Termite Group 1 (TG1):
uncultured Termite group 1 bacterium phylotype Rs-D17.
Termites, plus prokaryotic organisms and protists living in the termite gut, have been found to produce enzymes involved in cellulose digestion.
The bacterial colonies found in the termite gut produce large quantities of hydrogen as a byproduct of cellulose digestion.
A better understanding of these pathways could significantly aid research into renewable sources of energy.
30th Dec 2008
New article describing SUPERFAMILY, updated superfamily functional annotation, new eukaryotic genomes:
A new article describing the web site and database has been published in Nucleic Acids Research
Christine Vogel has updated her functional annotation of superfamilies to SCOP version 1.73.
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.
During December over 25 new Eukaryotic genomes have been added to the database.
Added the ability to browse through the SCOP hierarchy to superfamilies and families.
Browse SCOP hierarchy in SUPERFAMILY Starting at the top of the SCOP hierarchy, one can browse through
the classes and folds to superfamilies and families of interest. These pages contain the SCOP
entries and where available expert annotation from
InterPro
(including Gene Ontology terms) and functional annotation from
Christine Vogel. At the bottom of the superfamily and family pages are a number of links
to other relevant pages elsewhere on this site.
10th Oct 2008
Martin Madera has published a paper describing PRC
in Bioinformatics.
PRC is a stand-alone program for scoring and aligning profile hidden Markov models (profile HMMs) of
protein families. PRC can read models produced by SAM and HMMER, two popular profile HMM packages,
as well as PSI-BLAST checkpoint files. To cite PRC:
29th Sept 2008
A new HMM library based on SCOP 1.73 is now available for download from the ftp site.
The 1.73 model library consists of 13,920 models representing 1,776 superfamilies.
Genome assignments will be added to a beta web site as they become available.
We will first add assignments for the main model organisms, followed by the most important animal genomes, then the remaining eukaryotes and finally the bacteria and archaea.
When all genomes have been updated the beta site will become the live site. Update: The beta web site is now the live site.
Genome combinations or specific clades can be displayed as if individual trees
had been produced. The data used is extracted from a single large tree
generated from a presence/absence matrix using protein domain architecture data
for all genomes in SUPERFAMILY. The PAUP
software is used to produce a single, large tree topology using both neighbour
joining or heuristic parsimony methods.
12th Sept 2008
Integrated similar domain architectures tool:
We have added a tool to find functionally similar proteins. Our approach
compares the domain architecture of interest with all the other domain
architectures in the SUPERFAMILY database. The 10 architectures which are
most similar to the architecture of interest are selected for display.
Documentation describing
the similarity function used to find domain architectures with similar genomic
distribution. Links to the similar domain architectures can be found on any
of the gene pages or the domain combination pages.
1st Sept 2008
Major update to TaxViz taxonomic distribution of domains tool:
Over 200 genome sequences for "model" organisms have been added since
TaxViz was initially integrated into the SUPERFAMILY web site.
This resulted in some TaxViz pages, being unusable
because they contained too
many genomes. We have corrected this problem by adding additional "subkingdom"
taxonomic groups for the largest kingdoms: metazoa (animals), euryarchaeota,
proteobacteria, firmicutes and actinobacteria.
Integrated domain assignments for the
Dictyostelium purpureum genome
from the JGI.
The dictyostelids are a group of cellular slime molds, or social amoebae, which
belong to the amoebozoa supergroup of eukaryotes that form a sister clade to the
fungi and animals. Under normal growth conditions the dictyostelids take the
individual amoeba form, but under starvation they from multicellular organisms.
Further details.
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.
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.
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.
Follow us on twitter
]
"biogeographical structure of the pan-genome of this species"
Browse SCOP hierarchy in SUPERFAMILY
Phylogenetic trees
