SUPERFAMILY 1.75 HMM library and genome assignments server

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Comparative Genomics Tools

Comparative genomics tools for the analysis of superfamily, and family, domains from across the tree of life.


Over- and under-represented domains

Over- and under-represented superfamilies for a genome, compared to groups of genomes.

Search for genome:

Eg. Homo sapiens

The group of genomes for comparison consists of several predefined choices, such as eukaryotes or archaebacteria, or any user-defined set of genomes (or a single genome), e.g. other strains of the same species.
Over-represented superfamilies have typically expanded as the organism specialised for its environmental niche; e.g. in Shewanella oneidensis, a Gram-negative bacterium with diverse respiratory strategies that are of potential use in bioremediation, the five most unusual superfamilies include multiheme cytochromes, porins and transferrins. Proteins in these superfamilies may provide interesting targets for investigation.
Links to the unusual superfamily and family domains are provided at the top of each genome page.

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Adjacent domain pair lists and graphs

Lists of pairs of superfamilies that occur next to each other in the domain architectures for a genome.

Search for genome:

Eg. Homo sapiens

Can be accessed by clicking on the "domain combinations" link at the top of each genome page. This list can be visualised in the form of a graph, by clicking on the Adjacent domain pairs logo (shown above) at the top of the domain pairs list pages. Nodes represent superfamilies labelled according to their SCOP classification, edges indicate superfamilies that occur next to each other in domain architectures, and arrows show the N-to-C terminal order. Node size and edge thickness are proportional to the number of proteins.
Users can remove from the initial list those pairs that are already present in proteins of known structure, or which also occur in other genomes. Lists, and graphs, for adjacent domain pairs in custom sets of genomes can be obtained by entering two letter genome codes into the "Custom genome sets" form on the adjacent domain pairs list page.
Warning: for the sake of clarity these graphs are limited to 1500 edges, so they may not be available for all genomes.

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Domain combinations in groups of genomes

Visual representation of all domain architectures a superfamily occurs in.

Search for superfamily:

Eg. C2H2 zinc fingers

From this representation, a clear picture of partner domains occuring with the superfamily of interest can be gained. Five groups of genomes are available for comparison: all, eukaryotic, bacterial, eubacterial and archaeal.
These pages can be navigated to by selecting the superfamily of interest from one of the genome assignment pages, and then following the Domain Combinations icon link (shown above). Alternatively, the logo link is also present on the SCOP hierarchy pages for each superfamily.

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Taxonomic visualisation of domain distribution

Distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom.

Search for superfamily/family:

Eg. C2H2 zinc fingers

sf - superfamily, fa - family

This gives an immediate impression of how superfamilies/families are restricted to certain kingdoms of life.
The TaxViz pages can be navigated to by selecting the superfamily, or family, of interest from one of the genome assignment pages, and then following the Taxonomic Distribution link at the top of the page. Alternatively, the logo link is also present on the SCOP hierarchy pages for each superfamily and family.

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Domain occurrence networks

Undirected domain occurrence network for a superfamily.

Search for superfamily:

Eg. C2H2 zinc fingers

Nodes in these networks represent genomes. Connections between nodes represent the presence of domain architectures, which contain the superfamily of interest, in both genomes. These networks convey the co-occurrence of domain architectures, for each superfamily, across the genomes included in SUPERFAMILY.
Again, the Domain occurrence network pages can be navigated to by selecting the superfamily of interest from one of the genome assignment pages, and then clicking the network logo (shown above) at the top of the page. Alternatively, the logo link is also present on the SCOP hierarchy pages for each superfamily.

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