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The SUPERFAMILY 1.75 database in 2014: a doubling of data.

Oates ME, Stahlhacke J, Vavoulis DV, Smithers B, Rackham OJ, Sardar AJ, Zaucha J, Thurlby N, Fang H, Gough J - Nucleic Acids Res. (2014)

Bottom Line: This tree is built with genomic-scale domain annotation data as before, but constantly updated when new species are introduced to the sequence library.Our Gene Ontology and other functional and phenotypic annotations previously reported have stood up to critical assessment by the function prediction community.We have now introduced these data in an integrated manner online at the level of an individual sequence, and--in the case of whole genomes--with enrichment analysis against a taxonomically defined background.

View Article: PubMed Central - PubMed

Affiliation: Computer Science, University of Bristol, Bristol, BS8 1UB, UK Matt.Oates@bristol.ac.uk.

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Summary of all genome updates and additions at the level of taxonomic Class since the release of SUPERFAMILY 1.75. Eukarya in red, Archaea in green and Bacteria in blue. The size of each pie chart is log scaled based on the number of proteomes within each Class. Light colouration is the proportion of genomes that have been added to the database within a Class, and the dark colouration represents updated genomes. The grey colouring seen in Eukarya represents the relatively few genomes to not have been altered since the release of 1.75.
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Figure 1: Summary of all genome updates and additions at the level of taxonomic Class since the release of SUPERFAMILY 1.75. Eukarya in red, Archaea in green and Bacteria in blue. The size of each pie chart is log scaled based on the number of proteomes within each Class. Light colouration is the proportion of genomes that have been added to the database within a Class, and the dark colouration represents updated genomes. The grey colouring seen in Eukarya represents the relatively few genomes to not have been altered since the release of 1.75.

Mentions: In Figure 1 we present SUPERFAMILY's curated complete proteomes coverage over the tree of all sequenced life collapsed to the rank of Class as defined by the NCBI taxonomy. This does not include all of the species-specific annotations we serve as part of UniProt proteomes collection, but does include collections from NCBI RefSeq (as of 13 August 2014) (12) and Ensembl (release 76) (13) as well as hundreds of complete proteomes we have acquired from various individual sources (upon publication). Of special note is that SUPERFAMILY now provides assignments to the latest assembly of Human GRCh38 thanks to its recent inclusion in Ensembl. The new Human assembly has 61% of sequences with at least one domain annotation, and 44% of all amino acids being annotated with SCOP domains.


The SUPERFAMILY 1.75 database in 2014: a doubling of data.

Oates ME, Stahlhacke J, Vavoulis DV, Smithers B, Rackham OJ, Sardar AJ, Zaucha J, Thurlby N, Fang H, Gough J - Nucleic Acids Res. (2014)

Summary of all genome updates and additions at the level of taxonomic Class since the release of SUPERFAMILY 1.75. Eukarya in red, Archaea in green and Bacteria in blue. The size of each pie chart is log scaled based on the number of proteomes within each Class. Light colouration is the proportion of genomes that have been added to the database within a Class, and the dark colouration represents updated genomes. The grey colouring seen in Eukarya represents the relatively few genomes to not have been altered since the release of 1.75.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383889&req=5

Figure 1: Summary of all genome updates and additions at the level of taxonomic Class since the release of SUPERFAMILY 1.75. Eukarya in red, Archaea in green and Bacteria in blue. The size of each pie chart is log scaled based on the number of proteomes within each Class. Light colouration is the proportion of genomes that have been added to the database within a Class, and the dark colouration represents updated genomes. The grey colouring seen in Eukarya represents the relatively few genomes to not have been altered since the release of 1.75.
Mentions: In Figure 1 we present SUPERFAMILY's curated complete proteomes coverage over the tree of all sequenced life collapsed to the rank of Class as defined by the NCBI taxonomy. This does not include all of the species-specific annotations we serve as part of UniProt proteomes collection, but does include collections from NCBI RefSeq (as of 13 August 2014) (12) and Ensembl (release 76) (13) as well as hundreds of complete proteomes we have acquired from various individual sources (upon publication). Of special note is that SUPERFAMILY now provides assignments to the latest assembly of Human GRCh38 thanks to its recent inclusion in Ensembl. The new Human assembly has 61% of sequences with at least one domain annotation, and 44% of all amino acids being annotated with SCOP domains.

Bottom Line: This tree is built with genomic-scale domain annotation data as before, but constantly updated when new species are introduced to the sequence library.Our Gene Ontology and other functional and phenotypic annotations previously reported have stood up to critical assessment by the function prediction community.We have now introduced these data in an integrated manner online at the level of an individual sequence, and--in the case of whole genomes--with enrichment analysis against a taxonomically defined background.

View Article: PubMed Central - PubMed

Affiliation: Computer Science, University of Bristol, Bristol, BS8 1UB, UK Matt.Oates@bristol.ac.uk.

Show MeSH