Ensembl se “extiende” por el árbol taxonómico

Publicado por José María Fernández el 23 abril, 2009

Hace unos días mi amigo Javito me mandó desde el EBI el anuncio de la aparición de versiones especializadas de Ensembl en no vertebrados. Ensembl es el principal centro de integración de información genómica de organismos, y hasta hace relativamente poco estaba principalmente centrado en mamíferos. Desde entonces se ha ido generalizando a otros tipos de vertebrados (como el gallo) u organismos eucariotas (como C. Elegans o la mosca de la fruta), albergando a día de hoy información detallada de más de 50 organismos.

En esta nueva versión de Ensembl va a haber sitios extendidos especializados en no-vertebrados de las ramas taxonómicas de las bacterias (http://bacteria.ensembl.org/), protistas (http://protists.ensembl.org/) y metazoos (http://metazoa.ensembl.org/). Además, a lo largo del verano aparecerán sitios especializados para hongos y plantas. También la versión estándar de Ensembl sufre una mejora, a través de la web de Ensembl Genomes (http://www.ensemblgenomes.org/), cuya información estará coordinada con todas las webs de Ensembl, permitiendo análisis comparativos multigenómicos.

El anuncio original viene a continuación:

We are delighted to announce the forthcoming release of Ensembl Bacteria, Ensembl Protists and Ensembl Metazoa, the first sites to be launched as part of the EBI's "Ensembl Genomes" project to extend the use of the Ensembl browser to non-vertebrate genomes.

These following site are available:

http://bacteria.ensembl.orghttp://protists.ensembl.orghttp://metazoa.ensembl.org

Additional sites for fungi and plants are in development and will be launched during the summer of this year.

In the Ensembl Genomes project, we are aiming to do two things: firstly to work with particular communities to support the bioinformatic analysis of genome-scale data; and secondly, to provide an integrative portal to data from species of scientific interest from across the taxonomic space. In pursuit of both these aims, we will re-use and extend the proven Ensembl software system, that has been developed by EBI and the Wellcome Trust Sanger Institute in the context of vertebrate genomics.

As with Ensembl, Ensembl Genomes will provide access to DNA and protein sequence, positional and functional annotation of protein-coding and non-protein coding genes, repeat analysis and other features and statistics. An interesting feature made available with the release of Ensembl Genomes is the inclusion of a multi-way comparative genomic analysis performed using a selection of species from bacteria to humans, and the production of gene trees showing the inferred ancestral relationships within deeply conserved protein families. Comparative resources are also provided at a narrower level (for example, DNA and protein-based analyses of individual bacterial clades). In partnership with collaborators, we are working on capturing gene expression, and population-scale variation data, in a number of contexts. More generally, we anticipate the ongoing enrichment of these resources through the integration of increasing quantities of high throughput data now becoming routinely available for all species.

Ensembl Genomes will provide access to data through the usual routes supported for vertebrate data; web-based browser, FTP site, programmatic API, DAS, and BioMart-style data warehouse; as well as text and sequence-based search.

We look forward to working with you as future producers and consumers of data. More information about the project is available at http://www.ensemblgenomes.org. We will be happy to receive any feedback you might wish to offer us at helpdesk@ensemblgenomes.org.

------------------------------------------------------------------Dr. Paul KerseyTeam Leader, PANDA DataflowEMBL-European Bioinformatics Institute Tel: +44-(0)1223-494601Wellcome Trust Genome Campus, Hinxton Fax: +44-(0)1223-494468Cambridge CB10 1SD, UK