title: Ensembl comparative genomics resources.
abstract: Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, flicek@ebi.ac.uk javier.herrero@ucl.ac.uk muffato@ebi.ac.uk.
authors.forename: Javier
authors.initials: J
authors.lastname: Herrero
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Muffato
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD.
authors.forename: Kathryn
authors.initials: K
authors.lastname: Beal
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD.
authors.forename: Stephen
authors.initials: S
authors.lastname: Fitzgerald
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD.
authors.forename: Leo
authors.initials: L
authors.lastname: Gordon
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD.
authors.forename: Miguel
authors.initials: M
authors.lastname: Pignatelli
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD.
authors.forename: Albert J
authors.initials: AJ
authors.lastname: Vilella
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA.
authors.forename: Stephen M J
authors.initials: SM
authors.lastname: Searle
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA.
authors.forename: Ridwan
authors.initials: R
authors.lastname: Amode
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA.
authors.forename: Simon
authors.initials: S
authors.lastname: Brent
authors.affiliation: Eagle Genomics Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK, and Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
authors.forename: William
authors.initials: W
authors.lastname: Spooner
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA.
authors.forename: Eugene
authors.initials: E
authors.lastname: Kulesha
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD.
authors.forename: Andrew
authors.initials: A
authors.lastname: Yates
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, flicek@ebi.ac.uk.
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D016678:Genome; D023281:Genomics; D006801:Humans; D010802:Phylogeny; D011786:Quality Control; D022661:RNA, Untranslated / Q000235:genetics; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D018076:DNA, Complementary; D022661:RNA, Untranslated