|
|
SUPERFAMILY Description
SUPERFAMILY is a database of structural and functional protein annotations for all completely sequenced organisms.
A domain is the smallest unit of evolution; a large protein can be split into smaller domains.
Domains can occur by themselves or in combination with other domains. A superfamily groups together domains of different
families which have a common evolutionary ancestor based on structural, functional and evolutionary data.
The SUPERFAMILY web site and database provides protein domain assignments, at the SCOP
'superfamily' and 'family' levels, for the predicted protein sequences in over 900 organisms,
(plus sequence collections such as UniProt).
Please contact us if you think we have missed any organisms.
SUPERFAMILY domain assignments
are generated using an expert curated set of profile hidden Markov models. All models and structural assignments are available for
browsing and download. Sophisticated tools are provided for the analysis of superfamily (and family) domain assignments.
SUPERFAMILY Description cont ...
Major Features
| Sequence search |
Submit your protein, or DNA, sequence for superfamily and family level classification.
|
| Keyword search |
Search for superfamily names, family names, species names, sequence IDs,
SCOP IDs,
PDB IDs and hidden Markov model IDs.
|
| Domain assignments |
Domain assignments, alignments and architectures for completely sequenced
eukaryotic, and
prokaryotic organisms.
Additional sequence collections
are also included.
|
| Comparative genomics tools |
Browse unusual (over- and under-represented) superfamilies and families,
adjacent domain pair lists and graphs, unique domain pairs, domain combinations,
domain architecture co-occurrence networks and domain distribution across taxonomic kingdoms for each organism.
|
| Genome statistics |
For each genome: number of sequences, number of sequences with assignment,
percentage of sequences with assignment, percentage total sequence coverage, number of domains assigned,
number of superfamilies assigned, number of families assigned, average superfamily size,
percentage produced by duplication, average sequence length, average length matched and number of domain pairs.
|
| Superfamily annotation |
InterPro have added abstracts for 1,052 superfamilies,
and 763 superfamilies have some gene ontology annotation.
|
| Functional annotation |
Functional annotation of
SCOP 1.69 superfamilies. By
Christine Vogel.
|
| Profile comparison |
For finding remote domain matches. Available when the sequence search fails to find a significant match.
Profile comparison (PRC) for aligning and scoring two profile hidden Markov
models by Martin Madera.
|
| Hidden Markov models |
Produce SCOP domain assignments for your
sequences using the SUPERFAMILY models. HMM visualisation by
Martin Madera,
e.g. model 0045110.
|
| Web services |
Distributed Annotation Server and linking to SUPERFAMILY.
|
| Downloads |
Sequences, assignments, models, MySQL database and scripts - updated weekly.
|
Recent news
More details on recent updates to SUPERFAMILY can be found in the news archive.
|
