EBI Groups Ensembl Genomes Team

Ensembl Genomes Team

The Ensembl Genomes team develops services for non-vertebrate genomes, as part of the nucleotide section of Protein and Nucleotide Database (PANDA) Group. The team is led by Paul Kersey.

Ensembl Genomes

The Ensembl Genomes project utilises the Ensembl software infrastructure (originally developed in the Ensembl project), to provide access to genome-scale data from non-vertebrate species, working in partnershsip with experts from the relevant scientific communities.

VectorBase

We are one of six partners in VectorBase, a NIH NAIAD-funded Bioinformatics Resource Center for the Invertebrate Vectors of Human Pathogens. The EBI's involvement in VectorBase is coordinated by Daniel Lawson.

Microme

The team is coordinating the Microme project, a 14-partner large infrastructure project funded by the European Commission to develop a high-throughput resource for bacterial metabolic pathways and models.

PomBase

We have recentlyreceived funding with the University of Cambridge and University College London from the Wellcome Trust to establish PomBase, a model organism database for the fission yeast Schizosaccharomyces pombe.

Curtain

Curtain is an assembler of next generation sequence, developed by Matthias Haimel in the team. Curtain is a Java wrapper around next-generation assemblers such as Velvet which allows the incremental introduction of read-pair information into the assembly process. This enables the assembly of larger genomes than would otherwise be possible within existing memory constraints.

A pre-alpha release (0.1.0) of curtain is available here: http://code.google.com/p/curtain/. Documentation will be available shortly.

Other projects

We are partners in INFRAVEC, a project to build research infrastructures for the genetic control of mosquitoes; and EURASNET, a European Network of Excellence focused on alternative splicing. In collaboration with Richard Mott and Paula Kover we have BBSRC funding to study genetic variation in Arabidopsis thaliana; the BBSRC is also funding work on the development of next generation assembly tools, with a specific focus on potential applications in cereal plants.

The team is also responsible for running the Integr8, Genome Reviews and IPI projects, an earlier generation of resources for species with completely deciphered genomes, which will shortly be discontinued in favour of Ensembl Genomes.