The Ensembl automatic gene annotation system.

By Val Curwen, Eduardo Eyras, T. Daniel Andrews, Laura Clarke, Emmanuel Mongin, S. Searle, Michele E. Clamp. Genome Research, 2004

428 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/283bfd23d0d6963a20b515a14743a2e0021d9a57

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Citations in the corpus

Ensembl 2012 (2011, methodology): “These annotations are a merged gene set consisting of the output of the Ensembl evidence-based automatic pipeline (21) and the manual annotation from the Havana project (22).”
Ensembl 2007 (2006, methodology): “One such strategy is the creation of ‘mini’ sequences (11) which remove regions thought to be intronic from the final alignment step.”
Ensembl 2013 (2012, methodology): “For some of these species, the RNA-seq data were added after a standard gene annotation process (21), whereas for other species, the data were added as an integral part of the genebuild process.”
The Ensembl gene annotation system (2016, methodology): “(48), we described passing ‘MiniSeqs’ to GeneWise.”
The Ensembl Regulatory Build (2015, background): “The Ensembl framework, which currently holds a consistent relation database of gene transcripts [41], variants [42], and now regulatory elements will be a natural home for this key component of cell biology.”
Using native and syntenically mapped cDNA alignments to improve de novo gene finding (2008, background): “The gene predictions for human can be browsed and downloaded at the UCSC Genome Browser (http:// genome.ucsc.edu) Contact: mstanke@gwdg.de Supplementary information: Supplementary data are available at Bioinformatics online.”
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data (2010, methodology): “Several different gene annotation systems, including RefSeq genes, UCSC Genes and the Ensembl genes, can be utilized for 13), ANNOVAR will download the FASTA sequences from Ensembl as they were not available from the UCSC Genome Browser.”
Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver (2007, positive): “Transcript sequences were extracted from Ensembl using the ensembl–Perl–API ( 33 ).”
Comparative Genomics (2007, positive): “Powerful pipelines for gene annotations have been developed that combine both evidence-based and ab initio methods; one of the most widely used is the Ensembl automatic gene annotation system (Curwen et al. 2004).”
The UCSC Genome Browser database: 2019 update (2018, neutral): “Ensembl gene models are built through an automated pipeline and they are defined through genome coordinates, so they do not have to be mapped to a genome (19).”
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes (2007, methodology): “After that, the selected protein sequences of each species were aligned again with T-coffee to generate the final multiple alignments.”
DNA methylation profiling of human chromosomes 6, 20 and 22 (2006, methodology): “Amplicons were selected and classified into six categories (5′ UTR, exonic, intronic, ECR, Sp1 and 'other') based on Ensemb”
Detection of splice junctions from paired-end RNA-seq data by SpliceMap (2010, background): “In total, SpliceMap found 151 317 exon junctions, including 23 020 novel junctions, which were not reported in RefSeq (19), Ensembl (20) and KnownGene (21).”