EBI launches integrated genome and proteome browser
EBI launches Integr8, a new browser that allows biologists to fully exploit the wealth of information available in completely sequenced genomes and their predicted proteomes.
Through freely available databases such as those produced by the EBI and its collaborators, researchers now have access to huge amount of information on genes and proteins. But having access to the data is only part of the battle: to make new biological discoveries they need to be able to browse and search the data in an intuitive way.
“Integr8 brings together information on genomes and proteomes that previously was only available from different sources,” explains Paul Kersey, who coordinated the development of Integr8. “Although coding sequences, protein sequences and protein structures could be obtained from different databases, they were not linked in a systematic way. Integr8 provides a single point of access for information about genomes and the proteins they encode, and new ways to visualize the data. This makes it easier for biologists with no expertise in computer science to go straight to the information that they need.”
The first thing you see when you open the Integr8 web page at www.ebi.ac.uk/integr8 is a pie chart summarizing the 179 species – ranging from archaea to humans – whose genomes and proteomes have been Integr8ed. The site provides an easy way to quickly assess the molecular biology of a species: the nature of its genome, the protein families it contains [and those it does not contain], and the functional classification of its proteome [using the Gene Ontology]. The proteins produced by each organism have been clustered according to sequence similarity. This allows the quick identification of ‘singleton’ proteins [proteins whose sequence is unrelated to any others in the organism] and large or unclassified protein families within each species.
You can also view the latest publications on an organism, a list of all protein structures solved in that species, and comparisons with other species. Downloading the proteome set for a given organism is also straightforward. Other features include the ability to select your own ñbasketî of organisms to search, perform customized comparative analyses, and extract information from several databases in a single query using BioMart, a new EBI tool for complex queries.
“Integr8 represents the culmination of several years’ work on many data resources,” concludes Kersey. “We hope it will help biologists everywhere to make exciting new discoveries from genomic and proteomic data.”
Integr8 has been developed as part of the TEMBLOR project, funded by the European Commission.
