Ensembl se «extiende» por el árbol taxonómico
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.org
http://protists.ensembl.org
http://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.
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Dr. Paul Kersey
Team Leader, PANDA Dataflow
EMBL-European Bioinformatics Institute Tel: +44-(0)1223-494601
Wellcome Trust Genome Campus, Hinxton Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK