Ensembl 2009

By Tim J. P. Hubbard, Bronwen L. Aken, S. Ayling, B. Ballester, Kathryn M Beal, E. Bragin, Simon Brent, Yuan Chen, P. Clapham, Laura Clarke and 48 more. Nucleic Acids Res., 2008

549 citations recorded by the source corpus.

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).

Subfields: Molecular Biology, Plant Science

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Citations in the corpus

Ensembl variation resources (2010, methodology): “Ensembl [11], University of California at Santa Cruz (UCSC) [12,13] and the National Center for Biotechnology Information (NCBI) [14] have expertise in the storage and manipulation of biological data and have developed genome browsers and other methods to archive and display these data alongside…”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, methodology): “Fully sequenced genomes in STRING are imported from RefSeq (45) and Ensembl (46), as well as from a number of dedicated sites, and are hand-screened for completeness and non-redundancy.”
ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments (2010, methodology): “ArrayExpress has been importing selected GEO (3) Data sets (GDS) in order to provide uniﬁed queries across public data and for integration with European Bioinformatics Institute databases such as Ensembl (9).”
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons (2011, methodology): “Detecting frameshifts in coding sequences from public databases As a last proof-of-concept example, we used the properties of MACSE to detect undocumented frameshifts in the EnsEMBL public sequence database [40].”
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data (2010, methodology): “Both AltAnalyze and DomainGraph rely on locally installed databases based on annotation ﬁles provided by Aﬀymetrix and the corresponding builds of the Ensembl database (19).”